diff --git a/pom.xml b/pom.xml
index 63517947..079d68f3 100644
--- a/pom.xml
+++ b/pom.xml
@@ -295,6 +295,11 @@ under the License.
       <artifactId>commons-io</artifactId>
       <version>2.20.0</version>
     </dependency>
+    <dependency>
+      <groupId>org.apache.maven.scm</groupId>
+      <artifactId>maven-scm-api</artifactId>
+      <version>2.1.0</version>
+    </dependency>
 
     <!-- dependencies to annotations -->
     <dependency>
diff --git a/src/main/java/org/apache/maven/plugins/site/deploy/AbstractDeployMojo.java b/src/main/java/org/apache/maven/plugins/site/deploy/AbstractDeployMojo.java
index f280cdd0..daeaa040 100644
--- a/src/main/java/org/apache/maven/plugins/site/deploy/AbstractDeployMojo.java
+++ b/src/main/java/org/apache/maven/plugins/site/deploy/AbstractDeployMojo.java
@@ -37,6 +37,7 @@
 import org.apache.maven.plugins.annotations.Parameter;
 import org.apache.maven.plugins.site.AbstractSiteMojo;
 import org.apache.maven.project.MavenProject;
+import org.apache.maven.scm.provider.ScmUrlUtils;
 import org.apache.maven.settings.Proxy;
 import org.apache.maven.settings.Server;
 import org.apache.maven.settings.Settings;
@@ -492,6 +493,66 @@ private static String getFullName(MavenProject project) {
                 + project.getVersion() + ')';
     }
 
+    /**
+     * Extracts the provider-specific URL from an SCM URL for comparison purposes.
+     * For non-SCM URLs, returns the original URL.
+     * For SCM URLs with SCP-like syntax (e.g., git@github.com:user/repo.git),
+     * converts them to a comparable format.
+     * For hierarchical SCM systems like SVN, normalizes the scheme to enable
+     * proper comparison of URLs that differ only in http vs https.
+     *
+     * @param url the URL to process
+     * @return the provider-specific URL for SCM URLs, or the original URL otherwise
+     */
+    static String extractComparableUrl(String url) {
+        if (url != null && url.startsWith("scm:")) {
+            // Extract the SCM provider (e.g., "git", "svn")
+            String provider = ScmUrlUtils.getProvider(url);
+
+            // Extract the provider-specific part of the SCM URL
+            // For example: "scm:git:https://github.com/user/repo.git" -> "https://github.com/user/repo.git"
+            String providerSpecificPart = ScmUrlUtils.getProviderSpecificPart(url);
+            if (providerSpecificPart != null && !providerSpecificPart.isEmpty()) {
+                // Handle SCP-like Git syntax (e.g., git@github.com:user/repo.git or user@host:path)
+                // Convert it to a more standard format for comparison
+                // Note: This is a heuristic check - we look for the pattern of user@host:path
+                // where the colon comes after the @ symbol and is followed by a path
+                if (providerSpecificPart.contains("@")
+                        && !providerSpecificPart.startsWith("http://")
+                        && !providerSpecificPart.startsWith("https://")
+                        && !providerSpecificPart.startsWith("ssh://")) {
+                    // Find the @ symbol and look for the first : after it that's not part of a URL scheme
+                    int atIndex = providerSpecificPart.lastIndexOf('@');
+                    int colonIndex = providerSpecificPart.indexOf(':', atIndex);
+
+                    // Verify this looks like SCP syntax: user@host:path
+                    // The colon should come after @ and before the end
+                    if (atIndex >= 0 && colonIndex > atIndex + 1 && colonIndex < providerSpecificPart.length() - 1) {
+                        String host = providerSpecificPart.substring(atIndex + 1, colonIndex);
+                        String path = providerSpecificPart.substring(colonIndex + 1);
+                        // Convert to a pseudo-URL format for comparison
+                        // Note: IPv6 addresses in brackets are handled by this approach
+                        // as the brackets will be preserved in the host part
+                        return "ssh://" + host + "/" + path;
+                    }
+                }
+
+                // For hierarchical VCS systems like SVN, normalize the scheme to allow
+                // comparison of URLs that differ only in http vs https
+                // SVN repositories can be accessed via both protocols and should be considered the same
+                if ("svn".equalsIgnoreCase(provider) && providerSpecificPart.startsWith("https://")) {
+                    // Normalize https to http for SVN URLs to enable proper comparison
+                    return "http" + providerSpecificPart.substring(5);
+                }
+
+                // Return the provider-specific part as-is for standard URLs or
+                // if SCP syntax conversion is not applicable
+                return providerSpecificPart;
+            }
+        }
+        return url;
+    }
+
     /**
      * Extract the distributionManagement site of the top level parent of the given MavenProject.
      * This climbs up the project hierarchy and returns the site of the last project
@@ -523,8 +584,12 @@ protected MavenProject getTopLevelProject(MavenProject project) throws MojoExecu
             }
 
             // MSITE-600
-            URIPathDescriptor siteURI = new URIPathDescriptor(URIEncoder.encodeURI(site.getUrl()), "");
-            URIPathDescriptor oldSiteURI = new URIPathDescriptor(URIEncoder.encodeURI(oldSite.getUrl()), "");
+            // MSITE-1033: For SCM URLs, extract the provider-specific part for comparison
+            String siteUrlToCompare = extractComparableUrl(site.getUrl());
+            String oldSiteUrlToCompare = extractComparableUrl(oldSite.getUrl());
+
+            URIPathDescriptor siteURI = new URIPathDescriptor(URIEncoder.encodeURI(siteUrlToCompare), "");
+            URIPathDescriptor oldSiteURI = new URIPathDescriptor(URIEncoder.encodeURI(oldSiteUrlToCompare), "");
 
             if (!siteURI.sameSite(oldSiteURI.getBaseURI())) {
                 return oldProject;
diff --git a/src/test/java/org/apache/maven/plugins/site/deploy/AbstractDeployMojoTest.java b/src/test/java/org/apache/maven/plugins/site/deploy/AbstractDeployMojoTest.java
new file mode 100644
index 00000000..bd7a0540
--- /dev/null
+++ b/src/test/java/org/apache/maven/plugins/site/deploy/AbstractDeployMojoTest.java
@@ -0,0 +1,211 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.maven.plugins.site.deploy;
+
+import org.apache.maven.model.DistributionManagement;
+import org.apache.maven.model.Site;
+import org.apache.maven.plugin.MojoExecutionException;
+import org.apache.maven.project.MavenProject;
+import org.junit.Test;
+
+import static org.junit.Assert.assertEquals;
+
+/**
+ * Tests for AbstractDeployMojo.
+ */
+public class AbstractDeployMojoTest {
+
+    /**
+     * Test that getTopLevelProject correctly handles SCM URLs with different repositories.
+     * This is the test case for MSITE-1033.
+     */
+    @Test
+    public void testGetTopLevelProjectWithDifferentScmUrls() throws Exception {
+        // Create a mock deploy mojo
+        TestDeployMojo mojo = new TestDeployMojo();
+
+        // Create child project with SCM URL
+        MavenProject childProject =
+                createProjectWithSite("child", "scm:git:git@github.com:codehaus-plexus/plexus-sec-dispatcher.git/");
+
+        // Create parent project with different SCM URL
+        MavenProject parentProject =
+                createProjectWithSite("parent", "scm:git:https://github.com/codehaus-plexus/plexus-pom.git/");
+
+        // Set up the parent-child relationship
+        childProject.setParent(parentProject);
+
+        // Call getTopLevelProject - it should return childProject, not parentProject
+        // because the SCM URLs point to different repositories
+        MavenProject topProject = mojo.getTopLevelProject(childProject);
+
+        // The top project should be the child project itself since the parent has a different site
+        assertEquals("Top project should be child project due to different SCM URLs", childProject, topProject);
+    }
+
+    /**
+     * Test that getTopLevelProject correctly handles SCM URLs with the same repository.
+     */
+    @Test
+    public void testGetTopLevelProjectWithSameScmUrls() throws Exception {
+        // Create a mock deploy mojo
+        TestDeployMojo mojo = new TestDeployMojo();
+
+        // Create child project with SCM URL
+        MavenProject childProject =
+                createProjectWithSite("child", "scm:git:https://github.com/codehaus-plexus/plexus-pom.git/child");
+
+        // Create parent project with same base SCM URL
+        MavenProject parentProject =
+                createProjectWithSite("parent", "scm:git:https://github.com/codehaus-plexus/plexus-pom.git/");
+
+        // Set up the parent-child relationship
+        childProject.setParent(parentProject);
+
+        // Call getTopLevelProject - it should return parentProject
+        // because the SCM URLs point to the same repository
+        MavenProject topProject = mojo.getTopLevelProject(childProject);
+
+        // The top project should be the parent project since they share the same site
+        assertEquals("Top project should be parent project due to same SCM base URL", parentProject, topProject);
+    }
+
+    /**
+     * Test that getTopLevelProject correctly handles non-SCM URLs.
+     */
+    @Test
+    public void testGetTopLevelProjectWithNonScmUrls() throws Exception {
+        // Create a mock deploy mojo
+        TestDeployMojo mojo = new TestDeployMojo();
+
+        // Create child project with regular URL
+        MavenProject childProject = createProjectWithSite("child", "https://example.com/site/child");
+
+        // Create parent project with same base URL
+        MavenProject parentProject = createProjectWithSite("parent", "https://example.com/site/");
+
+        // Set up the parent-child relationship
+        childProject.setParent(parentProject);
+
+        // Call getTopLevelProject - it should return parentProject
+        MavenProject topProject = mojo.getTopLevelProject(childProject);
+
+        // The top project should be the parent project since they share the same site
+        assertEquals("Top project should be parent project for regular URLs", parentProject, topProject);
+    }
+
+    /**
+     * Test that getTopLevelProject correctly handles SCM URLs with standard https format.
+     */
+    @Test
+    public void testGetTopLevelProjectWithHttpsScmUrls() throws Exception {
+        // Create a mock deploy mojo
+        TestDeployMojo mojo = new TestDeployMojo();
+
+        // Create child project with https SCM URL
+        MavenProject childProject = createProjectWithSite("child", "scm:git:https://github.com/user/repo1.git/");
+
+        // Create parent project with different https SCM URL (different domain)
+        MavenProject parentProject = createProjectWithSite("parent", "scm:git:https://gitlab.com/user/repo2.git/");
+
+        // Set up the parent-child relationship
+        childProject.setParent(parentProject);
+
+        // Call getTopLevelProject - it should return childProject
+        // because the SCM URLs point to different repositories
+        MavenProject topProject = mojo.getTopLevelProject(childProject);
+
+        // The top project should be the child project itself since the parent has a different site
+        assertEquals("Top project should be child project due to different https SCM URLs", childProject, topProject);
+    }
+
+    /**
+     * Test that extractComparableUrl properly handles SVN URLs with different schemes but same host.
+     * For SVN (hierarchical VCS), URLs with different schemes (http vs https) should be normalized
+     * to the same scheme to allow URIPathDescriptor.sameSite() to recognize them as the same site.
+     * Note: The paths may differ (one being a subpath of another), but as long as scheme, host, and port
+     * are the same, URIPathDescriptor.sameSite() will correctly identify them as the same site.
+     */
+    @Test
+    public void testExtractComparableUrlForSvnUrls() throws Exception {
+        // Extract and normalize both URLs
+        String url1 = AbstractDeployMojo.extractComparableUrl("scm:svn:http://svn.apache.org/repos/asf/maven/website");
+        String url2 = AbstractDeployMojo.extractComparableUrl(
+                "scm:svn:https://svn.apache.org/repos/asf/maven/website/components");
+
+        // Both should be normalized to http scheme
+        assertEquals("http://svn.apache.org/repos/asf/maven/website", url1);
+        assertEquals("http://svn.apache.org/repos/asf/maven/website/components", url2);
+
+        // Now verify they would be considered the same site by creating projects with these URLs
+        TestDeployMojo mojo = new TestDeployMojo();
+        MavenProject childProject =
+                createProjectWithSite("child", "scm:svn:https://svn.apache.org/repos/asf/maven/website/components");
+        MavenProject parentProject =
+                createProjectWithSite("parent", "scm:svn:http://svn.apache.org/repos/asf/maven/website");
+        childProject.setParent(parentProject);
+
+        // The parent should be returned as the top project since they share the same SVN site
+        MavenProject topProject = mojo.getTopLevelProject(childProject);
+        assertEquals(
+                "Top project should be parent due to normalized SVN URLs pointing to same site",
+                parentProject,
+                topProject);
+    }
+
+    private MavenProject createProjectWithSite(String artifactId, String siteUrl) {
+        MavenProject project = new MavenProject();
+        project.setGroupId("org.apache.maven.test");
+        project.setArtifactId(artifactId);
+        project.setVersion("1.0");
+        project.setName(artifactId);
+
+        DistributionManagement distributionManagement = new DistributionManagement();
+        Site site = new Site();
+        site.setId("test-site");
+        site.setUrl(siteUrl);
+        distributionManagement.setSite(site);
+        project.setDistributionManagement(distributionManagement);
+
+        return project;
+    }
+
+    /**
+     * Test implementation of AbstractDeployMojo for testing.
+     */
+    private static class TestDeployMojo extends AbstractDeployMojo {
+        @Override
+        protected boolean isDeploy() {
+            return true;
+        }
+
+        @Override
+        protected String determineTopDistributionManagementSiteUrl() throws MojoExecutionException {
+            return "test";
+        }
+
+        @Override
+        protected Site determineDeploySite() throws MojoExecutionException {
+            Site site = new Site();
+            site.setId("test");
+            site.setUrl("test");
+            return site;
+        }
+    }
+}