diff --git a/script/tool/lib/src/common/package_command.dart b/script/tool/lib/src/common/package_command.dart
index c16783db3a7e..21aeaffeeaaa 100644
--- a/script/tool/lib/src/common/package_command.dart
+++ b/script/tool/lib/src/common/package_command.dart
@@ -436,16 +436,26 @@ abstract class PackageCommand extends Command<void> {
       packages = <String>{currentPackageName};
     }
 
-    Set<String> excludedPackageNames = getExcludedPackageNames();
-
-    final Set<String> filter =
-        _expandYamlInPackageList(getStringListArg(_filterPackagesArg));
-    if (filter.isNotEmpty) {
-      final List<String> sortedList = filter.toList()..sort();
+    final Set<String> excludedPackageNames = getExcludedPackageNames();
+    final bool hasFilter = argResults?.wasParsed(_filterPackagesArg) ?? false;
+    final Set<String>? excludeAllButPackageNames = hasFilter
+        ? _expandYamlInPackageList(getStringListArg(_filterPackagesArg))
+        : null;
+    if (excludeAllButPackageNames != null &&
+        excludeAllButPackageNames.isNotEmpty) {
+      final List<String> sortedList = excludeAllButPackageNames.toList()
+        ..sort();
       print('--$_filterPackagesArg is excluding packages that are not '
           'included in: ${sortedList.join(',')}');
-      excludedPackageNames =
-          excludedPackageNames.union(packages.difference(filter));
+    }
+    // Returns true if a package that could be identified by any of
+    // `possibleNames` should be excluded.
+    bool isExcluded(Set<String> possibleNames) {
+      if (excludedPackageNames.intersection(possibleNames).isNotEmpty) {
+        return true;
+      }
+      return excludeAllButPackageNames != null &&
+          excludeAllButPackageNames.intersection(possibleNames).isEmpty;
     }
 
     for (final Directory dir in <Directory>[
@@ -459,7 +469,7 @@ abstract class PackageCommand extends Command<void> {
           if (packages.isEmpty || packages.contains(p.basename(entity.path))) {
             yield PackageEnumerationEntry(
                 RepositoryPackage(entity as Directory),
-                excluded: excludedPackageNames.contains(entity.basename));
+                excluded: isExcluded(<String>{entity.basename}));
           }
         } else if (entity is Directory) {
           // Look for Dart packages under this top-level directory; this is the
@@ -481,9 +491,7 @@ abstract class PackageCommand extends Command<void> {
                   packages.intersection(possibleMatches).isNotEmpty) {
                 yield PackageEnumerationEntry(
                     RepositoryPackage(subdir as Directory),
-                    excluded: excludedPackageNames
-                        .intersection(possibleMatches)
-                        .isNotEmpty);
+                    excluded: isExcluded(possibleMatches));
               }
             }
           }
diff --git a/script/tool/test/common/package_command_test.dart b/script/tool/test/common/package_command_test.dart
index e269b063886a..d7742658afb8 100644
--- a/script/tool/test/common/package_command_test.dart
+++ b/script/tool/test/common/package_command_test.dart
@@ -825,6 +825,80 @@ packages/plugin3/plugin3.dart
 
         expect(command.plugins, unorderedEquals(<String>[plugin1.path]));
       });
+
+      test(
+          'honors --filter-packages-to flag when a file is changed that makes '
+          'all packages potentially changed', () async {
+        processRunner.mockProcessesForExecutable['git-diff'] =
+            <FakeProcessInfo>[
+          FakeProcessInfo(MockProcess(stdout: '''
+.ci.yaml
+''')),
+        ];
+        final RepositoryPackage plugin1 =
+            createFakePlugin('plugin1', packagesDir.childDirectory('plugin1'));
+        createFakePlugin('plugin2', packagesDir);
+        createFakePlugin('plugin3', packagesDir);
+        await runCapturingPrint(runner, <String>[
+          'sample',
+          '--filter-packages-to=plugin1',
+          '--base-sha=main',
+          '--run-on-changed-packages'
+        ]);
+
+        expect(command.plugins, unorderedEquals(<String>[plugin1.path]));
+      });
+
+      test('--filter-packages-to handles federated plugin groups', () async {
+        processRunner.mockProcessesForExecutable['git-diff'] =
+            <FakeProcessInfo>[
+          FakeProcessInfo(MockProcess(stdout: '''
+packages/a_plugin/a_plugin/lib/foo.dart
+packages/a_plugin/a_plugin_impl/lib/foo.dart
+packages/a_plugin/a_plugin_platform_interface/lib/foo.dart
+''')),
+        ];
+        final Directory groupDir = packagesDir.childDirectory('a_plugin');
+        final RepositoryPackage plugin1 =
+            createFakePlugin('a_plugin', groupDir);
+        final RepositoryPackage plugin2 =
+            createFakePlugin('a_plugin_impl', groupDir);
+        final RepositoryPackage plugin3 =
+            createFakePlugin('a_plugin_platform_interface', groupDir);
+        await runCapturingPrint(runner, <String>[
+          'sample',
+          '--filter-packages-to=a_plugin',
+          '--base-sha=main',
+          '--run-on-changed-packages'
+        ]);
+
+        expect(
+            command.plugins,
+            unorderedEquals(
+                <String>[plugin1.path, plugin2.path, plugin3.path]));
+      });
+
+      test('--filter-packages-to and --exclude work together', () async {
+        processRunner.mockProcessesForExecutable['git-diff'] =
+            <FakeProcessInfo>[
+          FakeProcessInfo(MockProcess(stdout: '''
+.ci.yaml
+''')),
+        ];
+        final RepositoryPackage plugin1 =
+            createFakePlugin('plugin1', packagesDir.childDirectory('plugin1'));
+        createFakePlugin('plugin2', packagesDir);
+        createFakePlugin('plugin3', packagesDir);
+        await runCapturingPrint(runner, <String>[
+          'sample',
+          '--filter-packages-to=plugin1,plugin2',
+          '--exclude=plugin2',
+          '--base-sha=main',
+          '--run-on-changed-packages'
+        ]);
+
+        expect(command.plugins, unorderedEquals(<String>[plugin1.path]));
+      });
     });
 
     group('test run-on-dirty-packages', () {