diff --git a/script/tool/CHANGELOG.md b/script/tool/CHANGELOG.md
index 234700ab5a..dec218e2ba 100644
--- a/script/tool/CHANGELOG.md
+++ b/script/tool/CHANGELOG.md
@@ -5,6 +5,9 @@
   dependencies to path-based dependencies.
 - Adds a (hidden) `--run-on-dirty-packages` flag for use with
   `make-deps-path-based` in CI.
+- Fix `federation-safety-check` handling of plugin deletion, and of top-level
+  files in unfederated plugins whose names match federated plugin heuristics
+  (e.g., `packages/foo/foo_android.iml`).
 
 ## 0.7.3
 
diff --git a/script/tool/lib/src/federation_safety_check_command.dart b/script/tool/lib/src/federation_safety_check_command.dart
index 200f9c3f48..df9d86892e 100644
--- a/script/tool/lib/src/federation_safety_check_command.dart
+++ b/script/tool/lib/src/federation_safety_check_command.dart
@@ -81,7 +81,8 @@ class FederationSafetyCheckCommand extends PackageLoopingCommand {
       // Count the top-level plugin as changed.
       _changedPlugins.add(packageName);
       if (relativeComponents[0] == packageName ||
-          relativeComponents[0].startsWith('${packageName}_')) {
+          (relativeComponents.length > 1 &&
+              relativeComponents[0].startsWith('${packageName}_'))) {
         packageName = relativeComponents.removeAt(0);
       }
 
@@ -178,6 +179,10 @@ class FederationSafetyCheckCommand extends PackageLoopingCommand {
       String pubspecRepoRelativePosixPath) async {
     final File pubspecFile = childFileWithSubcomponents(
         packagesDir.parent, p.posix.split(pubspecRepoRelativePosixPath));
+    if (!pubspecFile.existsSync()) {
+      // If the package was deleted, nothing will be published.
+      return false;
+    }
     final Pubspec pubspec = Pubspec.parse(pubspecFile.readAsStringSync());
     if (pubspec.publishTo == 'none') {
       return false;
diff --git a/script/tool/lib/src/make_deps_path_based_command.dart b/script/tool/lib/src/make_deps_path_based_command.dart
index 04869639cf..5ee42848a8 100644
--- a/script/tool/lib/src/make_deps_path_based_command.dart
+++ b/script/tool/lib/src/make_deps_path_based_command.dart
@@ -196,19 +196,27 @@ dependency_overrides:
   Future<Set<String>> _getNonBreakingUpdatePackages() async {
     final GitVersionFinder gitVersionFinder = await retrieveVersionFinder();
     final String baseSha = await gitVersionFinder.getBaseSha();
-    print('Finding changed packages relative to "$baseSha"\n');
+    print('Finding changed packages relative to "$baseSha"...');
 
     final Set<String> changedPackages = <String>{};
-    for (final String path in await gitVersionFinder.getChangedFiles()) {
+    for (final String changedPath in await gitVersionFinder.getChangedFiles()) {
       // Git output always uses Posix paths.
-      final List<String> allComponents = p.posix.split(path);
+      final List<String> allComponents = p.posix.split(changedPath);
       // Only pubspec changes are potential publishing events.
       if (allComponents.last != 'pubspec.yaml' ||
           allComponents.contains('example')) {
         continue;
       }
       final RepositoryPackage package =
-          RepositoryPackage(packagesDir.fileSystem.file(path).parent);
+          RepositoryPackage(packagesDir.fileSystem.file(changedPath).parent);
+      // Ignored deleted packages, as they won't be published.
+      if (!package.pubspecFile.existsSync()) {
+        final String directoryName = p.posix.joinAll(path.split(path.relative(
+            package.directory.absolute.path,
+            from: packagesDir.path)));
+        print('  Skipping $directoryName; deleted.');
+        continue;
+      }
       final String packageName = package.parsePubspec().name;
       if (!await _hasNonBreakingVersionChange(package)) {
         // Log packages that had pubspec changes but weren't included for ease
diff --git a/script/tool/test/federation_safety_check_command_test.dart b/script/tool/test/federation_safety_check_command_test.dart
index e23485fbc8..126aa8b41c 100644
--- a/script/tool/test/federation_safety_check_command_test.dart
+++ b/script/tool/test/federation_safety_check_command_test.dart
@@ -352,4 +352,64 @@ void main() {
       ]),
     );
   });
+
+  test('handles top-level files that match federated package heuristics',
+      () async {
+    final Directory plugin = createFakePlugin('foo', packagesDir);
+
+    final String changedFileOutput = <File>[
+      // This should be picked up as a change to 'foo', and not crash.
+      plugin.childFile('foo_bar.baz'),
+    ].map((File file) => file.path).join('\n');
+    processRunner.mockProcessesForExecutable['git-diff'] = <io.Process>[
+      MockProcess(stdout: changedFileOutput),
+    ];
+
+    final List<String> output =
+        await runCapturingPrint(runner, <String>['federation-safety-check']);
+
+    expect(
+      output,
+      containsAllInOrder(<Matcher>[
+        contains('Running for foo...'),
+      ]),
+    );
+  });
+
+  test('handles deletion of an entire plugin', () async {
+    // Simulate deletion, in the form of diffs for packages that don't exist in
+    // the filesystem.
+    final String changedFileOutput = <File>[
+      packagesDir.childDirectory('foo').childFile('pubspec.yaml'),
+      packagesDir
+          .childDirectory('foo')
+          .childDirectory('lib')
+          .childFile('foo.dart'),
+      packagesDir
+          .childDirectory('foo_platform_interface')
+          .childFile('pubspec.yaml'),
+      packagesDir
+          .childDirectory('foo_platform_interface')
+          .childDirectory('lib')
+          .childFile('foo.dart'),
+      packagesDir.childDirectory('foo_web').childFile('pubspec.yaml'),
+      packagesDir
+          .childDirectory('foo_web')
+          .childDirectory('lib')
+          .childFile('foo.dart'),
+    ].map((File file) => file.path).join('\n');
+    processRunner.mockProcessesForExecutable['git-diff'] = <io.Process>[
+      MockProcess(stdout: changedFileOutput),
+    ];
+
+    final List<String> output =
+        await runCapturingPrint(runner, <String>['federation-safety-check']);
+
+    expect(
+      output,
+      containsAllInOrder(<Matcher>[
+        contains('Ran for 0 package(s)'),
+      ]),
+    );
+  });
 }
diff --git a/script/tool/test/make_deps_path_based_command_test.dart b/script/tool/test/make_deps_path_based_command_test.dart
index 29e4f724b3..bdd2139b23 100644
--- a/script/tool/test/make_deps_path_based_command_test.dart
+++ b/script/tool/test/make_deps_path_based_command_test.dart
@@ -173,6 +173,29 @@ void main() {
       );
     });
 
+    test('no-ops for no deleted packages', () async {
+      final String changedFileOutput = <File>[
+        // A change for a file that's not on disk simulates a deletion.
+        packagesDir.childDirectory('foo').childFile('pubspec.yaml'),
+      ].map((File file) => file.path).join('\n');
+      processRunner.mockProcessesForExecutable['git-diff'] = <io.Process>[
+        MockProcess(stdout: changedFileOutput),
+      ];
+
+      final List<String> output = await runCapturingPrint(runner, <String>[
+        'make-deps-path-based',
+        '--target-dependencies-with-non-breaking-updates'
+      ]);
+
+      expect(
+        output,
+        containsAllInOrder(<Matcher>[
+          contains('Skipping foo; deleted.'),
+          contains('No target dependencies'),
+        ]),
+      );
+    });
+
     test('includes bugfix version changes as targets', () async {
       const String newVersion = '1.0.1';
       final Directory package =