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 e2c6eff88c3..03e34916ebe 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
@@ -17,6 +17,7 @@
 package org.jetbrains.kotlin.cli.jvm.compiler
 
 import com.intellij.openapi.project.Project
+import com.intellij.openapi.application.ApplicationManager
 import com.intellij.openapi.util.io.JarUtil
 import com.intellij.openapi.vfs.VfsUtilCore
 import com.intellij.openapi.vfs.VirtualFile
@@ -264,7 +265,9 @@ object KotlinToJVMBytecodeCompiler {
             }
 
             // Clear package caches (see KotlinJavaPsiFacade)
-            (PsiManager.getInstance(environment.project).modificationTracker as? PsiModificationTrackerImpl)?.incCounter()
+            ApplicationManager.getApplication().runWriteAction {
+                (PsiManager.getInstance(environment.project).modificationTracker as? PsiModificationTrackerImpl)?.incCounter()
+            }
 
             // Clear all diagnostic messages
             configuration[CLIConfigurationKeys.MESSAGE_COLLECTOR_KEY]?.clear()
diff --git a/plugins/annotation-processing/src/org/jetbrains/kotlin/annotation/processing/AnnotationProcessingExtension.kt b/plugins/annotation-processing/src/org/jetbrains/kotlin/annotation/processing/AnnotationProcessingExtension.kt
index dbca20b0801..11dc198d540 100755
--- a/plugins/annotation-processing/src/org/jetbrains/kotlin/annotation/processing/AnnotationProcessingExtension.kt
+++ b/plugins/annotation-processing/src/org/jetbrains/kotlin/annotation/processing/AnnotationProcessingExtension.kt
@@ -16,6 +16,7 @@
 
 package org.jetbrains.kotlin.annotation
 
+import com.intellij.openapi.application.ApplicationManager
 import com.intellij.openapi.project.Project
 import com.intellij.openapi.vfs.StandardFileSystems
 import com.intellij.psi.JavaPsiFacade
@@ -291,7 +292,9 @@ abstract class AbstractAnnotationProcessingExtension(
         }
         
         // Update the platform caches
-        (psiManager().modificationTracker as? PsiModificationTrackerImpl)?.incCounter()
+        ApplicationManager.getApplication().runWriteAction {
+            (psiManager().modificationTracker as? PsiModificationTrackerImpl)?.incCounter()
+        }
         
         // Find generated files
         val localFileSystem = StandardFileSystems.local()