diff --git a/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/KotlinToJVMBytecodeCompiler.kt b/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/KotlinToJVMBytecodeCompiler.kt
index 26ac641283b..aeabc058d29 100644
--- a/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/KotlinToJVMBytecodeCompiler.kt
+++ b/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/KotlinToJVMBytecodeCompiler.kt
@@ -59,11 +59,13 @@ import org.jetbrains.kotlin.modules.TargetId
 import org.jetbrains.kotlin.name.FqName
 import org.jetbrains.kotlin.progress.ProgressIndicatorAndCompilationCanceledStatus
 import org.jetbrains.kotlin.psi.KtFile
+import org.jetbrains.kotlin.resolve.jvm.KotlinJavaPsiFacade
 import org.jetbrains.kotlin.script.tryConstructClassFromStringArgs
 import org.jetbrains.kotlin.utils.newLinkedHashMapWithExpectedSize
 import java.io.File
 import java.lang.reflect.InvocationTargetException
 import java.net.URLClassLoader
+import javax.swing.SwingUtilities
 
 object KotlinToJVMBytecodeCompiler {
     private fun writeOutput(
@@ -302,10 +304,7 @@ object KotlinToJVMBytecodeCompiler {
                 environment.updateClasspath(result.additionalJavaRoots.map { JavaSourceRoot(it, null) })
             }
 
-            // Clear package caches (see KotlinJavaPsiFacade)
-            ApplicationManager.getApplication().runWriteAction {
-                (PsiManager.getInstance(environment.project).modificationTracker as? PsiModificationTrackerImpl)?.incCounter()
-            }
+            KotlinJavaPsiFacade.getInstance(environment.project).clearPackageCaches()
 
             // Clear all diagnostic messages
             configuration[CLIConfigurationKeys.MESSAGE_COLLECTOR_KEY]?.clear()
diff --git a/compiler/frontend.java/src/org/jetbrains/kotlin/resolve/jvm/KotlinJavaPsiFacade.java b/compiler/frontend.java/src/org/jetbrains/kotlin/resolve/jvm/KotlinJavaPsiFacade.java
index 6d4716c776b..2ec44f2c0d9 100644
--- a/compiler/frontend.java/src/org/jetbrains/kotlin/resolve/jvm/KotlinJavaPsiFacade.java
+++ b/compiler/frontend.java/src/org/jetbrains/kotlin/resolve/jvm/KotlinJavaPsiFacade.java
@@ -96,6 +96,10 @@ public class KotlinJavaPsiFacade {
         });
     }
 
+    public void clearPackageCaches() {
+        packageCache = null;
+    }
+
     public LightModifierList getEmptyModifierList() {
         return emptyModifierList;
     }