diff --git a/packages/bazel/src/ng_package/packager.ts b/packages/bazel/src/ng_package/packager.ts
index 6ef447ac88..f72fa1b5eb 100644
--- a/packages/bazel/src/ng_package/packager.ts
+++ b/packages/bazel/src/ng_package/packager.ts
@@ -102,6 +102,13 @@ function main(args: string[]): number {
   const modulesManifest = JSON.parse(modulesManifestArg);
   const dtsBundles: string[] = dtsBundleArg.split(',').filter(s => !!s);
 
+  /**
+   * List of known `package.json` fields which provide information about
+   * supported package formats and their associated entry paths.
+   */
+  const knownFormatPackageJsonFields =
+      ['main', 'fesm2015', 'esm2015', 'typings', 'module', 'es2015'];
+
   if (readmeMd) {
     copyFile(readmeMd, out);
   }
@@ -324,11 +331,10 @@ function main(args: string[]): number {
     const packageName = parsedPackage['name'];
     const moduleData = modulesManifest[packageName];
 
-    // We don't want to modify the "package.json" if we guessed the entry-point
-    // paths and there is a custom "package.json" for that package already. Module
-    // data will be only undefined if the package name comes from a non-generated
-    // "package.json". In that case we want to leave the file untouched as well.
-    if (!moduleData || moduleData.guessedPaths && !isGeneratedPackageJson) {
+    // If a package json file has been discovered that does not match any
+    // module in the manifest, we report a warning as most likely the target
+    // is configured incorrectly (e.g. missing `module_name` attribute).
+    if (!moduleData) {
       // Ideally we should throw here, as we got an entry point that doesn't
       // have flat module metadata / bundle index, so it may have been an
       // ng_module that's missing a module_name attribute.
@@ -342,6 +348,19 @@ function main(args: string[]): number {
       return JSON.stringify(parsedPackage, null, 2);
     }
 
+    // If we guessed the index paths for a module, and it contains an explicit `package.json`
+    // file that already sets format properties, we skip automatic insertion of format
+    // properties but report a warning in case properties have been set by accident.
+    if (moduleData.guessedPaths && !isGeneratedPackageJson &&
+        hasExplicitFormatProperties(parsedPackage)) {
+      console.error('WARNING: `package.json` explicitly sets format properties (like `main`).');
+      console.error(
+          '    Skipping automatic insertion of format properties as explicit ' +
+          'format properties are set.');
+      console.error('    Ignore this warning if explicit properties are set intentionally.');
+      return JSON.stringify(parsedPackage, null, 2);
+    }
+
     // Derive the paths to the files from the hard-coded names we gave them.
     // TODO(alexeagle): it would be better to transfer this information from the place
     // where we created the filenames, via the modulesManifestArg
@@ -377,6 +396,12 @@ function main(args: string[]): number {
     return [relativePath, dir, basename + '.js'].join('/');
   }
 
+  /** Whether the package explicitly sets any of the format properties (like `main`). */
+  function hasExplicitFormatProperties(parsedPackage: {[key: string]: string}): boolean {
+    return Object.keys(parsedPackage)
+        .some(propertyName => knownFormatPackageJsonFields.includes(propertyName));
+  }
+
   /** Creates metadata re-export file for a secondary entry-point. */
   function createMetadataReexportFile(
       entryPointName: string, metadataFile: string, packageName: string) {