diff --git a/core/packaging/flags.mk b/core/packaging/flags.mk
index a77956bdea..4693bcd6d8 100644
--- a/core/packaging/flags.mk
+++ b/core/packaging/flags.mk
@@ -18,7 +18,7 @@
 #
 
 # TODO: Should we do all of the images in $(IMAGES_TO_BUILD)?
-_FLAG_PARTITIONS := product system system_ext vendor
+_FLAG_PARTITIONS := product system vendor
 
 
 # -----------------------------------------------------------------
@@ -28,7 +28,6 @@ _FLAG_PARTITIONS := product system system_ext vendor
 # $(1): built aconfig flags file (out)
 # $(2): installed aconfig flags file (out)
 # $(3): the partition (in)
-# $(4): input aconfig files for the partition (in)
 define generate-partition-aconfig-flag-file
 $(eval $(strip $(1)): PRIVATE_OUT := $(strip $(1)))
 $(eval $(strip $(1)): PRIVATE_IN := $(strip $(4)))
@@ -36,12 +35,14 @@ $(strip $(1)): $(ACONFIG) $(strip $(4))
 	mkdir -p $$(dir $$(PRIVATE_OUT))
 	$$(if $$(PRIVATE_IN), \
 		$$(ACONFIG) dump --dedup --format protobuf --out $$(PRIVATE_OUT) \
-			--filter container:$$(strip $(3)) $$(addprefix --cache ,$$(PRIVATE_IN)), \
+			--filter container:$(strip $(3)) \
+			$$(addprefix --cache ,$$(PRIVATE_IN)), \
 		echo -n > $$(PRIVATE_OUT) \
 	)
 $(call copy-one-file, $(1), $(2))
 endef
 
+
 # Create a summary file of build flags for each partition
 # $(1): built aconfig flags file (out)
 # $(2): installed aconfig flags file (out)
@@ -59,16 +60,22 @@ $(strip $(1)): $(ACONFIG) $(strip $(3))
 $(call copy-one-file, $(1), $(2))
 endef
 
-
 $(foreach partition, $(_FLAG_PARTITIONS), \
 	$(eval aconfig_flag_summaries_protobuf.$(partition) := $(PRODUCT_OUT)/$(partition)/etc/aconfig_flags.pb) \
 	$(eval $(call generate-partition-aconfig-flag-file, \
-				$(TARGET_OUT_FLAGS)/$(partition)/aconfig_flags.pb, \
-				$(aconfig_flag_summaries_protobuf.$(partition)), \
-				$(partition), \
-				$(sort $(foreach m,$(call register-names-for-partition, $(partition)), \
+			$(TARGET_OUT_FLAGS)/$(partition)/aconfig_flags.pb, \
+			$(aconfig_flag_summaries_protobuf.$(partition)), \
+			$(partition), \
+			$(sort \
+				$(foreach m, $(call register-names-for-partition, $(partition)), \
 					$(ALL_MODULES.$(m).ACONFIG_FILES) \
-				)), \
+				) \
+				$(if $(filter system, $(partition)), \
+					$(foreach m, $(call register-names-for-partition, system_ext), \
+						$(ALL_MODULES.$(m).ACONFIG_FILES) \
+					) \
+				) \
+			) \
 	)) \
 )
 
@@ -175,4 +182,3 @@ $(foreach partition, $(_FLAG_PARTITIONS), \
 	$(eval aconfig_storage_flag_map.$(partition):=) \
 	$(eval aconfig_storage_flag_val.$(partition):=) \
 )
-
diff --git a/tools/aconfig/aconfig/src/commands.rs b/tools/aconfig/aconfig/src/commands.rs
index 1a14f6415a..797a893ff1 100644
--- a/tools/aconfig/aconfig/src/commands.rs
+++ b/tools/aconfig/aconfig/src/commands.rs
@@ -79,8 +79,18 @@ pub fn parse_flags(
             .read_to_string(&mut contents)
             .with_context(|| format!("failed to read {}", input.source))?;
 
-        let flag_declarations = aconfig_protos::flag_declarations::try_from_text_proto(&contents)
-            .with_context(|| input.error_context())?;
+        let mut flag_declarations =
+            aconfig_protos::flag_declarations::try_from_text_proto(&contents)
+                .with_context(|| input.error_context())?;
+
+        // system_ext flags should be treated as system flags as we are combining /system_ext
+        // and /system as one container
+        // TODO: remove this logic when we start enforcing that system_ext cannot be set as
+        // container in aconfig declaration files.
+        if flag_declarations.container() == "system_ext" {
+            flag_declarations.set_container(String::from("system"));
+        }
+
         ensure!(
             package == flag_declarations.package(),
             "failed to parse {}: expected package {}, got {}",