diff --git a/.changeset/new-pandas-perform.md b/.changeset/new-pandas-perform.md
new file mode 100644
index 0000000000..797f34d6df
--- /dev/null
+++ b/.changeset/new-pandas-perform.md
@@ -0,0 +1,5 @@
+---
+'@backstage/repo-tools': minor
+---
+
+Fix invalid path and malformed flags bugs in api-reports.ts
diff --git a/packages/repo-tools/src/commands/api-reports/api-reports.test.ts b/packages/repo-tools/src/commands/api-reports/api-reports.test.ts
index 955720c52e..94ae42d715 100644
--- a/packages/repo-tools/src/commands/api-reports/api-reports.test.ts
+++ b/packages/repo-tools/src/commands/api-reports/api-reports.test.ts
@@ -323,6 +323,24 @@ describe('buildApiReports', () => {
 
       expect(buildDocs).not.toHaveBeenCalled();
     });
+    it('should throw an error if a path does not exist', async () => {
+      const paths = ['packages/package-a', 'packages/package-c'];
+      const opts = {};
+
+      await expect(buildApiReports(paths, opts)).rejects.toThrow(
+        'Invalid paths provided: packages/package-c',
+      );
+    });
+    it('should throw an error if an option is malformed', async () => {
+      const paths = ['ae-undocumented'];
+      const opts = {
+        omitMessages: 'ae-wrong-input-file-type,',
+      };
+
+      await expect(buildApiReports(paths, opts)).rejects.toThrow(
+        'Invalid paths provided: ae-undocumented',
+      );
+    });
   });
   describe('allowWarnings', () => {
     it('should accept single path value', async () => {
diff --git a/packages/repo-tools/src/commands/api-reports/api-reports.ts b/packages/repo-tools/src/commands/api-reports/api-reports.ts
index 637cd86671..4e568102d9 100644
--- a/packages/repo-tools/src/commands/api-reports/api-reports.ts
+++ b/packages/repo-tools/src/commands/api-reports/api-reports.ts
@@ -48,6 +48,7 @@ export const buildApiReports = async (paths: string[] = [], opts: Options) => {
   const omitMessages = parseArrayOption(opts.omitMessages);
 
   const isAllPackages = !paths?.length;
+
   const selectedPackageDirs = await resolvePackagePaths({
     paths,
     include: opts.include,
@@ -130,5 +131,10 @@ export const buildApiReports = async (paths: string[] = [], opts: Options) => {
  * // returns []
  */
 function parseArrayOption(value: string | undefined) {
-  return value ? value.split(',').map(s => s.trim()) : [];
+  return value
+    ? value
+        .split(',')
+        .map(s => s.trim())
+        .filter(Boolean)
+    : [];
 }
diff --git a/packages/repo-tools/src/lib/paths.ts b/packages/repo-tools/src/lib/paths.ts
index 96fc92f035..0dcec32ff1 100644
--- a/packages/repo-tools/src/lib/paths.ts
+++ b/packages/repo-tools/src/lib/paths.ts
@@ -36,6 +36,23 @@ export async function resolvePackagePaths(
   const { paths: providedPaths, include, exclude } = options;
   let packages = await PackageGraph.listTargetPackages();
 
+  if (providedPaths && providedPaths.length > 0) {
+    const invalidPaths: string[] = [];
+    for (const path of providedPaths) {
+      const matches = packages.some(
+        ({ dir }) =>
+          new Minimatch(path).match(relativePath(paths.targetRoot, dir)) ||
+          isChildPath(dir, path),
+      );
+      if (!matches) {
+        invalidPaths.push(path);
+      }
+    }
+    if (invalidPaths.length > 0) {
+      throw new Error(`Invalid paths provided: ${invalidPaths.join(', ')}`);
+    }
+  }
+
   if (providedPaths && providedPaths.length > 0) {
     packages = packages.filter(({ dir }) =>
       providedPaths.some(