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 e25c5dff964..dd2370c15ec 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
@@ -410,7 +410,7 @@ object KotlinToJVMBytecodeCompiler {
             return if (versionIndex >= 0) substring(0, versionIndex) else this
         }
 
-        val runtimes = jvmClasspathRoots.filter { it.name == PathUtil.KOTLIN_JAVA_RUNTIME_JAR && it.exists() }
+        val runtimes = jvmClasspathRoots.map { it.canonicalFile }.filter { it.name == PathUtil.KOTLIN_JAVA_RUNTIME_JAR && it.exists() }
 
         val runtimeVersions = runtimes.map {
             JarUtil.getJarAttribute(it, Attributes.Name.IMPLEMENTATION_VERSION).orEmpty().removeIdeaVersionSuffix()
diff --git a/compiler/testData/cli/jvm/conflictingRuntimeVersion.out b/compiler/testData/cli/jvm/conflictingRuntimeVersion.out
index 9521d8c8be1..a2533c39072 100644
--- a/compiler/testData/cli/jvm/conflictingRuntimeVersion.out
+++ b/compiler/testData/cli/jvm/conflictingRuntimeVersion.out
@@ -1,4 +1,4 @@
-error: conflicting versions of Kotlin runtime on classpath: compiler/testData/cli/jvm/kotlin-runtime-4584-stub/kotlin-runtime.jar, $PROJECT_DIR$/lib/kotlin-runtime.jar
+error: conflicting versions of Kotlin runtime on classpath: $TESTDATA_DIR$/kotlin-runtime-4584-stub/kotlin-runtime.jar, $PROJECT_DIR$/lib/kotlin-runtime.jar
 compiler/testData/cli/jvm/conflictingRuntimeVersions.kt:1:9: error: unresolved reference: unresolvedFunction
 val f = unresolvedFunction()
         ^