diff --git a/jps/jps-plugin/jps-tests/test/org/jetbrains/kotlin/jps/build/KotlinJpsBuildTest.kt b/jps/jps-plugin/jps-tests/test/org/jetbrains/kotlin/jps/build/KotlinJpsBuildTest.kt
index 77c3968c5d7..82385cdf7f5 100644
--- a/jps/jps-plugin/jps-tests/test/org/jetbrains/kotlin/jps/build/KotlinJpsBuildTest.kt
+++ b/jps/jps-plugin/jps-tests/test/org/jetbrains/kotlin/jps/build/KotlinJpsBuildTest.kt
@@ -359,7 +359,7 @@ open class KotlinJpsBuildTest : AbstractKotlinJpsBuildTestCase() {
         buildAllModules().assertSuccessful()
 
         val sourceMapContent = File(getOutputDir(PROJECT_NAME), "$PROJECT_NAME.js.map").readText()
-        val expectedPath = "prefix-dir/pkg/test1.kt"
+        val expectedPath = "prefix-dir/src/pkg/test1.kt"
         assertTrue("Source map file should contain relative path ($expectedPath)", sourceMapContent.contains("\"$expectedPath\""))
 
         val librarySourceMapFile = File(getOutputDir(PROJECT_NAME), "lib/kotlin.js.map")
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 73780a77220..6b696ab58ac 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
@@ -67,6 +67,7 @@ import org.jetbrains.kotlin.progress.CompilationCanceledStatus
 import org.jetbrains.kotlin.utils.*
 import org.jetbrains.org.objectweb.asm.ClassReader
 import java.io.File
+import java.net.URI
 import java.util.*
 
 class KotlinBuilder : ModuleLevelBuilder(BuilderCategory.SOURCE_PROCESSOR) {
@@ -647,7 +648,10 @@ class KotlinBuilder : ModuleLevelBuilder(BuilderCategory.SOURCE_PROCESSOR) {
         val compilerSettings = JpsKotlinCompilerSettings.getCompilerSettings(representativeModule)
         val k2JsArguments = JpsKotlinCompilerSettings.getK2JsCompilerArguments(representativeModule)
 
-        val sourceRoots = KotlinSourceFileCollector.getRelevantSourceRoots(representativeTarget).map { it.file }
+        val sourceRoots = representativeModule.contentRootsList.urls
+                .map { URI.create(it) }
+                .filter { it.scheme == "file" }
+                .map { File(it) }
 
         val friendPaths = KotlinBuilderModuleScriptGenerator.getProductionModulesWhichInternalsAreVisible(representativeTarget).mapNotNull {
             val file = getOutputMetaFile(it, false)