diff --git a/src/BUILD b/src/BUILD
index 18b41e12902199..25d00a52514073 100644
--- a/src/BUILD
+++ b/src/BUILD
@@ -115,43 +115,46 @@ py_binary(
     deps = [":create_embedded_tools_lib"],
 )
 
+# The tools Bazel uses to compile Java.
+# TODO(#6316): Gradually remove the targets here.
+JAVA_TOOLS = [
+    "//third_party/jarjar:embedded_tools_srcs",
+    "//third_party/java/jdk/langtools:test-srcs",
+    "//third_party/java/proguard:embedded_tools",
+    "//src/java_tools/buildjar/java/com/google/devtools/build/buildjar/jarhelper:srcs",
+    "//src/tools/singlejar:embedded_tools",
+    "//src/java_tools/import_deps_checker/java/com/google/devtools/build/importdeps:embedded_tools",
+    "//third_party/ijar",
+    "//third_party/ijar:zipper",
+    "//third_party/ijar:embedded_tools",
+    "//third_party/java/jacoco:srcs",
+] + select({
+    "//src/conditions:arm": [],
+    "//conditions:default": [
+        "//src/tools/singlejar:singlejar_local",
+    ],
+})
+
 # TODO(philwo): Clean this up, once a Bazel that can run py_binary and sh_binary
 # in Skylark rules on Windows has been released.
 [filegroup(
     name = "embedded_tools" + suffix + "_srcs",
-    srcs = [
+    srcs = JAVA_TOOLS + [
                "BUILD.tools",
                "//tools:embedded_tools_srcs",
                "//third_party:gpl-srcs",
+               "//third_party/java/java_tools:java_tools",
                "//third_party/java/j2objc:embedded_tools_srcs",
-               "//third_party/jarjar:embedded_tools_srcs",
-               "//third_party/java/jdk/langtools:test-srcs",
-               "//third_party/java/proguard:embedded_tools",
                "//third_party/py/concurrent:srcs",
                "//third_party/py/gflags:srcs",
                "//third_party/py/six:srcs",
                "//src/conditions:embedded_tools",
-               "//src/java_tools/buildjar/java/com/google/devtools/build/buildjar/jarhelper:srcs",
                "//src/tools/android/java/com/google/devtools/build/android:embedded_tools",
                "//src/tools/launcher:srcs",
-               "//src/tools/singlejar:embedded_tools",
                "//src/main/cpp/util:embedded_tools",
                "//src/main/native:embedded_tools",
                "//src/main/protobuf:srcs",
-               "//src/java_tools/buildjar:JavaBuilderDeploy",
-               "//src/java_tools/buildjar:VanillaJavaBuilder_deploy.jar",
-               "//src/java_tools/buildjar/java/com/google/devtools/build/buildjar/genclass:GenClass_deploy.jar",
-               "//src/java_tools/import_deps_checker/java/com/google/devtools/build/importdeps:embedded_tools",
-               "//src/java_tools/junitrunner/java/com/google/testing/junit/runner:Runner_deploy.jar",
-               "//src/java_tools/junitrunner/java/com/google/testing/junit/runner:ExperimentalRunner_deploy.jar",
-               "//src/java_tools/junitrunner/java/com/google/testing/coverage:embedded_tools",
                "//third_party/def_parser:srcs",
-               "//third_party/ijar",
-               "//third_party/ijar:zipper",
-               "//third_party/ijar:embedded_tools",
-               "//src/java_tools/buildjar/java/com/google/devtools/build/java/turbine:turbine_direct",
-               "//src/java_tools/buildjar/java/com/google/devtools/build/java/turbine/javac:turbine_deploy.jar",
-               "//third_party/java/jacoco:srcs",
                "//third_party/zlib:embedded_tools",
            ] + select({
                "//src/conditions:darwin": [
@@ -169,13 +172,6 @@ py_binary(
                    "//third_party/def_parser:def_parser",
                ],
                "//conditions:default": [],
-           }) + select({
-               "//src/conditions:arm": [
-                   "//src/java_tools/singlejar:SingleJar_deploy.jar",
-               ],
-               "//conditions:default": [
-                   "//src/tools/singlejar:singlejar_local",
-               ],
            }) +
            jdk,
     visibility = [
diff --git a/src/java_tools/buildjar/BUILD b/src/java_tools/buildjar/BUILD
index 1723e23dd0a4e2..c08bbd2f345479 100644
--- a/src/java_tools/buildjar/BUILD
+++ b/src/java_tools/buildjar/BUILD
@@ -37,16 +37,6 @@ java_binary(
     runtime_deps = ["//src/java_tools/buildjar/java/com/google/devtools/build/buildjar:vanilla_java_builder"],
 )
 
-filegroup(
-    name = "JavaBuilderDeploy",
-    srcs = [":JavaBuilder_deploy.jar"],
-    tags = ["manual"],
-    visibility = [
-        ":buildjar_package_group",
-        "//src:__pkg__",
-    ],
-)
-
 filegroup(
     name = "bootstrap_VanillaJavaBuilder_deploy.jar",
     srcs = ["//src/java_tools/buildjar/java/com/google/devtools/build/buildjar:bootstrap_VanillaJavaBuilder_deploy.jar"],
diff --git a/src/java_tools/buildjar/java/com/google/devtools/build/java/turbine/BUILD b/src/java_tools/buildjar/java/com/google/devtools/build/java/turbine/BUILD
index 981c07577dfec1..17ec3012bf0514 100644
--- a/src/java_tools/buildjar/java/com/google/devtools/build/java/turbine/BUILD
+++ b/src/java_tools/buildjar/java/com/google/devtools/build/java/turbine/BUILD
@@ -11,14 +11,6 @@ java_binary(
     ],
 )
 
-filegroup(
-    name = "turbine_direct",
-    srcs = ["turbine_direct_binary_deploy.jar"],
-    visibility = [
-        "//:__subpackages__",
-    ],
-)
-
 filegroup(
     name = "srcs",
     srcs = glob(["**/*.java"]) + [
diff --git a/src/java_tools/junitrunner/java/com/google/testing/coverage/BUILD b/src/java_tools/junitrunner/java/com/google/testing/coverage/BUILD
index fa2f21b91517aa..c98c525cd4a66d 100644
--- a/src/java_tools/junitrunner/java/com/google/testing/coverage/BUILD
+++ b/src/java_tools/junitrunner/java/com/google/testing/coverage/BUILD
@@ -7,14 +7,6 @@ filegroup(
     srcs = glob(["**"]),
 )
 
-filegroup(
-    name = "embedded_tools",
-    srcs = [
-        "JacocoCoverage_jarjar_deploy.jar",
-    ],
-    tags = ["manual"],
-)
-
 # Bazel custom Jacoco runner used to provide proper initialization and lcov
 # report generation when using offline Jacoco instrumentation.
 # This target should not be used as a dependency (except when writing tests for