diff --git a/CleanSpec.mk b/CleanSpec.mk
index 7aba3526f..a2385e03b 100644
--- a/CleanSpec.mk
+++ b/CleanSpec.mk
@@ -722,6 +722,13 @@ $(call add-clean-step, find $(SOONG_OUT_DIR)/.intermediates -type d -name "andro
 # Remove 'media' command
 $(call add-clean-step, rm -rf $(PRODUCT_OUT)/system/bin/media)
 
+# Remove CtsShim apks from system partition, since the have been moved inside
+# the cts shim apex. Also remove the cts shim apex prebuilt since it has been
+# removed in flattened apexs configurations.
+$(call add-clean-step, rm -rf $(PRODUCT_OUT)/system/priv-app/CtsShimPrivPrebuilt)
+$(call add-clean-step, rm -rf $(PRODUCT_OUT)/system/app/CtsShimPrebuilt)
+$(call add-clean-step, rm -rf $(PRODUCT_OUT)/system/apex/com.android.apex.cts.shim.apex)
+
 # ************************************************
 # NEWER CLEAN STEPS MUST BE AT THE END OF THE LIST
 # ************************************************
diff --git a/target/product/base_system.mk b/target/product/base_system.mk
index 5c803ee35..0d752c3b9 100644
--- a/target/product/base_system.mk
+++ b/target/product/base_system.mk
@@ -51,7 +51,7 @@ PRODUCT_PACKAGES += \
     charger \
     cmd \
     com.android.adbd \
-    com.android.apex.cts.shim.v1_prebuilt \
+    com.android.apex.cts.shim.v1 \
     com.android.conscrypt \
     com.android.cronet \
     com.android.i18n \
@@ -72,8 +72,6 @@ PRODUCT_PACKAGES += \
     ContactsProvider \
     content \
     crash_dump \
-    CtsShimPrebuilt \
-    CtsShimPrivPrebuilt \
     debuggerd\
     device_config \
     dmctl \
diff --git a/target/product/updatable_apex.mk b/target/product/updatable_apex.mk
index bdaf54517..e5a647c20 100644
--- a/target/product/updatable_apex.mk
+++ b/target/product/updatable_apex.mk
@@ -17,6 +17,7 @@
 # Inherit this when the target needs to support updating APEXes
 
 ifneq ($(OVERRIDE_TARGET_FLATTEN_APEX),true)
+  PRODUCT_PACKAGES += com.android.apex.cts.shim.v1_prebuilt
   PRODUCT_PROPERTY_OVERRIDES := ro.apex.updatable=true
   TARGET_FLATTEN_APEX := false
 endif