diff --git a/jps/jps-plugin/src/org/jetbrains/kotlin/jps/build/KotlinBuilder.kt b/jps/jps-plugin/src/org/jetbrains/kotlin/jps/build/KotlinBuilder.kt
index 21650505dd2..212d7d1747f 100644
--- a/jps/jps-plugin/src/org/jetbrains/kotlin/jps/build/KotlinBuilder.kt
+++ b/jps/jps-plugin/src/org/jetbrains/kotlin/jps/build/KotlinBuilder.kt
@@ -380,7 +380,7 @@ class KotlinBuilder : ModuleLevelBuilder(BuilderCategory.SOURCE_PROCESSOR) {
                         rebuildAfterCacheVersionChanged[target] = true
                     }
 
-                    dataManager.withLookupStorage { it.clean() }
+                    dataManager.cleanLookupStorage(LOG)
                     return
                 }
                 CacheVersion.Action.REBUILD_CHUNK -> {
@@ -405,7 +405,7 @@ class KotlinBuilder : ModuleLevelBuilder(BuilderCategory.SOURCE_PROCESSOR) {
                 }
                 CacheVersion.Action.CLEAN_DATA_CONTAINER -> {
                     LOG.info("Clearing lookup cache")
-                    dataManager.withLookupStorage { it.clean() }
+                    dataManager.cleanLookupStorage(LOG)
                     cacheVersionsProvider.dataContainerVersion().clean()
                 }
                 else -> {
diff --git a/jps/jps-plugin/src/org/jetbrains/kotlin/jps/incremental/JpsLookupStorage.kt b/jps/jps-plugin/src/org/jetbrains/kotlin/jps/incremental/JpsLookupStorage.kt
index 1b565144a49..c68c128b36f 100644
--- a/jps/jps-plugin/src/org/jetbrains/kotlin/jps/incremental/JpsLookupStorage.kt
+++ b/jps/jps-plugin/src/org/jetbrains/kotlin/jps/incremental/JpsLookupStorage.kt
@@ -16,6 +16,7 @@
 
 package org.jetbrains.kotlin.jps.incremental
 
+import com.intellij.openapi.diagnostic.Logger
 import org.jetbrains.jps.builders.storage.BuildDataCorruptedException
 import org.jetbrains.jps.builders.storage.StorageProvider
 import org.jetbrains.jps.incremental.storage.BuildDataManager
@@ -24,13 +25,28 @@ import org.jetbrains.kotlin.incremental.LookupStorage
 import java.io.File
 import java.io.IOException
 
-@Synchronized
+private object LookupStorageLock
+
+fun BuildDataManager.cleanLookupStorage(log: Logger) {
+    synchronized(LookupStorageLock) {
+        try {
+            cleanTargetStorages(KotlinDataContainerTarget)
+        } catch (e: IOException) {
+            if (!dataPaths.getTargetDataRoot(KotlinDataContainerTarget).deleteRecursively()) {
+                log.debug("Could not clear lookup storage caches", e)
+            }
+        }
+    }
+}
+
 fun <T> BuildDataManager.withLookupStorage(fn: (LookupStorage) -> T): T {
-    try {
-        val lookupStorage = getStorage(KotlinDataContainerTarget, JpsLookupStorageProvider)
-        return fn(lookupStorage)
-    } catch (e: IOException) {
-        throw BuildDataCorruptedException(e)
+    synchronized(LookupStorageLock) {
+        try {
+            val lookupStorage = getStorage(KotlinDataContainerTarget, JpsLookupStorageProvider)
+            return fn(lookupStorage)
+        } catch (e: IOException) {
+            throw BuildDataCorruptedException(e)
+        }
     }
 }