diff --git a/packages/compiler-cli/ngcc/src/packages/entry_point_bundle.ts b/packages/compiler-cli/ngcc/src/packages/entry_point_bundle.ts
index bc369b5ada..dd770ae792 100644
--- a/packages/compiler-cli/ngcc/src/packages/entry_point_bundle.ts
+++ b/packages/compiler-cli/ngcc/src/packages/entry_point_bundle.ts
@@ -47,15 +47,14 @@ export function makeEntryPointBundle(
     mirrorDtsFromSrc: boolean = false,
     enableI18nLegacyMessageIdFormat: boolean = true): EntryPointBundle {
   // Create the TS program and necessary helpers.
+  const rootDir = entryPoint.package;
   const options: ts.CompilerOptions = {
     allowJs: true,
     maxNodeModuleJsDepth: Infinity,
-    noLib: true,
-    rootDir: entryPoint.path, ...pathMappings
+    noLib: true, rootDir, ...pathMappings
   };
   const srcHost = new NgccSourcesCompilerHost(fs, options, entryPoint.path);
   const dtsHost = new NgtscCompilerHost(fs, options);
-  const rootDirs = [absoluteFrom(entryPoint.path)];
 
   // Create the bundle programs, as necessary.
   const absFormatPath = fs.resolve(entryPoint.path, formatPath);
@@ -71,8 +70,11 @@ export function makeEntryPointBundle(
                              null;
   const isFlatCore = isCore && src.r3SymbolsFile === null;
 
-  return {entryPoint, format, rootDirs, isCore,
-          isFlatCore, src,    dts,      enableI18nLegacyMessageIdFormat};
+  return {
+    entryPoint,
+    format,
+    rootDirs: [rootDir], isCore, isFlatCore, src, dts, enableI18nLegacyMessageIdFormat
+  };
 }
 
 function computePotentialDtsFilesFromJsFiles(
diff --git a/packages/compiler-cli/ngcc/test/packages/entry_point_bundle_spec.ts b/packages/compiler-cli/ngcc/test/packages/entry_point_bundle_spec.ts
index 285a219e6f..67bfa6a76c 100644
--- a/packages/compiler-cli/ngcc/test/packages/entry_point_bundle_spec.ts
+++ b/packages/compiler-cli/ngcc/test/packages/entry_point_bundle_spec.ts
@@ -148,6 +148,16 @@ runInEachFileSystem(() => {
           name: _('/node_modules/internal/esm2015/src/internal.js'),
           contents: 'export function internal();'
         },
+
+        // A package with a secondary entry-point that has source files in a different tree
+        {
+          name: _('/node_modules/primary/secondary/index.d.ts'),
+          contents: 'export declare function secondary();'
+        },
+        {
+          name: _('/node_modules/primary/esm2015/secondary/index.js'),
+          contents: 'export function secondary();'
+        },
       ]);
     }
 
@@ -268,5 +278,24 @@ runInEachFileSystem(() => {
          expect(esm5bundle.dts !.program.getSourceFiles().map(sf => sf.fileName))
              .not.toContain(absoluteFrom('/node_modules/test/internal.d.ts'));
        });
+
+    it('should set the `rootDir` to the package path not the entry-point path', () => {
+      setupMockFileSystem();
+      const fs = getFileSystem();
+      const entryPoint: EntryPoint = {
+        name: 'secondary',
+        packageJson: {name: 'secondary'},
+        package: absoluteFrom('/node_modules/primary'),
+        path: absoluteFrom('/node_modules/primary/secondary'),
+        typings: absoluteFrom('/node_modules/primary/secondary/index.d.ts'),
+        compiledByAngular: true,
+        ignoreMissingDependencies: false,
+        generateDeepReexports: false,
+      };
+      const bundle = makeEntryPointBundle(
+          fs, entryPoint, './index.js', false, 'esm2015', /* transformDts */ true,
+          /* pathMappings */ undefined, /* mirrorDtsFromSrc */ true);
+      expect(bundle.rootDirs).toEqual([absoluteFrom('/node_modules/primary')]);
+    });
   });
 });