build.gradle with custom ndkBuild task

build.gradle

sourceSets.main {
    jni.srcDirs = [] //disable automatic ndk-build call
    jniLibs.srcDir 'src/main/jni'
}

task ndkBuild(type: Exec, description: 'Compile JNI source via NDK') {
    commandLine "<path to your ndk>/ndk-build",
            'NDK_PROJECT_PATH=build/intermediates/ndk',
            'NDK_LIBS_OUT=src/main/jniLibs',
            'APP_BUILD_SCRIPT=src/main/jni/Android.mk',
            'NDK_APPLICATION_MK=src/main/jni/Application.mk'
}
tasks.withType(JavaCompile) {
    compileTask -> compileTask.dependsOn ndkBuild
}