diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/KotlinGradlePluginIT.kt b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/KotlinGradlePluginIT.kt
index 4a9417fb344..6b3b695ff01 100644
--- a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/KotlinGradlePluginIT.kt
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/KotlinGradlePluginIT.kt
@@ -29,6 +29,7 @@ import java.io.File
 import java.util.zip.ZipFile
 import kotlin.test.assertEquals
 import kotlin.test.assertNotEquals
+import kotlin.test.assertNotNull
 import kotlin.test.assertTrue
 
 class KotlinGradleIT: BaseGradleIT() {
@@ -659,4 +660,60 @@ class KotlinGradleIT: BaseGradleIT() {
             }
         }
     }
-}
\ No newline at end of file
+
+    @Test
+    fun testSrcDirTaskDependency() {
+        Project("simpleProject", "4.1").apply {
+            setupWorkingDir()
+            File(projectDir, "build.gradle").appendText("""${'\n'}
+                task generateSources {
+                    outputs.dir('generated')
+                    doLast {
+                        def file = new File('generated/test/TestClass.java')
+                        file.parentFile.mkdirs()
+                        file.text = ""${'"'}
+                            package test;
+
+                            public class TestClass { }
+                        ""${'"'}
+                    }
+                }
+                sourceSets.main.java.srcDir(tasks.generateSources)
+                """.trimIndent())
+            File(projectDir, "src/main/kotlin/helloWorld.kt").appendText("""${'\n'}
+                fun usageOfGeneratedSource() = test.TestClass()
+                """.trimIndent())
+
+            build("build") {
+                assertSuccessful()
+            }
+        }
+    }
+
+    @Test
+    fun testSourceJar() {
+        Project("simpleProject", "4.1").apply {
+            setupWorkingDir()
+            val additionalSrcDir = "src/additional/kotlin/"
+
+            File(projectDir, additionalSrcDir).mkdirs()
+            File(projectDir, "$additionalSrcDir/additionalSource.kt").writeText("fun hello() = 123")
+
+            File(projectDir, "build.gradle").appendText("""${'\n'}
+                task sourcesJar(type: Jar) {
+                    from sourceSets.main.allSource
+                    classifier 'source'
+                    duplicatesStrategy = 'fail' // fail in case of Java source duplication, see KT-17564
+                }
+
+                sourceSets.main.kotlin.srcDir('$additionalSrcDir') // test that additional srcDir is included
+                """.trimIndent())
+
+            build("sourcesJar") {
+                assertSuccessful()
+                val sourcesJar = ZipFile(File(projectDir, "build/libs/simpleProject-source.jar"))
+                assertNotNull(sourcesJar.getEntry("additionalSource.kt"))
+            }
+        }
+    }
+}
diff --git a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/KotlinPlugin.kt b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/KotlinPlugin.kt
index d12a08e7ab7..30964a15dcc 100755
--- a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/KotlinPlugin.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/KotlinPlugin.kt
@@ -10,6 +10,7 @@ import org.gradle.api.*
 import org.gradle.api.artifacts.Configuration
 import org.gradle.api.file.ConfigurableFileCollection
 import org.gradle.api.file.FileCollection
+import org.gradle.api.file.SourceDirectorySet
 import org.gradle.api.logging.Logger
 import org.gradle.api.logging.Logging
 import org.gradle.api.plugins.InvalidPluginException
@@ -86,11 +87,30 @@ internal abstract class KotlinSourceSetProcessor<T : AbstractKotlinCompile<*>>(
 
     private fun addKotlinDirSetToSources() {
         val kotlinDirSet = kotlinSourceSet.kotlin
-        sourceSet.allJava.source(kotlinDirSet)
-        sourceSet.allSource.source(kotlinDirSet)
+
+        // Try to avoid duplicate Java sources in allSource:
+        val kotlinSrcDirsToAdd = filterOutJavaSrcDirsIfPossible(kotlinDirSet)
+
+        sourceSet.allJava.srcDirs(kotlinSrcDirsToAdd)
+        sourceSet.allSource.srcDirs(kotlinSrcDirsToAdd)
         sourceSet.resources.filter.exclude { it.file in kotlinDirSet }
     }
 
+    private fun filterOutJavaSrcDirsIfPossible(sourceDirectorySet: SourceDirectorySet): FileCollection {
+        // If the API used below is not available, fall back to not filtering the Java sources.
+        if (SourceDirectorySet::class.java.methods.none { it.name == "getSourceDirectories" }) {
+            return sourceDirectorySet
+        }
+
+        fun getSourceDirectories(sourceDirectorySet: SourceDirectorySet): FileCollection {
+            val method = SourceDirectorySet::class.java.getMethod("getSourceDirectories")
+            return method(sourceDirectorySet) as FileCollection
+        }
+
+        // Build a lazily-resolved file collection that filters out Java sources from sources of this sourceDirectorySet
+        return getSourceDirectories(sourceDirectorySet).minus(getSourceDirectories(sourceSet.java))
+    }
+
     private fun createKotlinCompileTask(): T {
         val name = sourceSet.getCompileTaskName(compileTaskNameSuffix)
         logger.kotlinDebug("Creating kotlin compile task $name")
@@ -129,6 +149,7 @@ internal class Kotlin2JvmSourceSetProcessor(
 
     override fun doTargetSpecificProcessing() {
         val aptConfiguration = project.createAptConfiguration(sourceSet.name, kotlinPluginVersion)
+        kotlinSourceSet.kotlin.source(sourceSet.java)
 
         project.afterEvaluate { project ->
             if (project != null) {
@@ -154,8 +175,6 @@ internal class Kotlin2JvmSourceSetProcessor(
                     removeAnnotationProcessingPluginClasspathEntry(kotlinTask)
                 }
 
-                sourceSet.java.srcDirs.forEach { kotlinSourceSet.kotlin.srcDir(it) }
-
                 // KotlinCompile.source(kotlinDirSet) should be called only after all java roots are added to kotlinDirSet
                 // otherwise some java roots can be ignored
                 kotlinTask.source(kotlinSourceSet.kotlin)