diff --git a/encoding/protobuf/parse.go b/encoding/protobuf/parse.go
index b962112ad..9e7f914f7 100644
--- a/encoding/protobuf/parse.go
+++ b/encoding/protobuf/parse.go
@@ -277,7 +277,11 @@ func (p *protoConverter) resolveTopScope(pos scanner.Position, name string, opti
 		if k == -1 {
 			i = len(name)
 		}
-		if m, ok := p.scope[0][name[:i]]; ok {
+		curName := name[:i]
+		if local, ok := strings.CutPrefix(curName, p.protoPkg+"."); ok {
+			curName = local
+		}
+		if m, ok := p.scope[0][curName]; ok {
 			if m.pkg != nil {
 				p.imported[m.pkg.qualifiedImportPath()] = true
 			}
diff --git a/encoding/protobuf/protobuf_test.go b/encoding/protobuf/protobuf_test.go
index c08696116..ad2aefe03 100644
--- a/encoding/protobuf/protobuf_test.go
+++ b/encoding/protobuf/protobuf_test.go
@@ -37,6 +37,7 @@ func TestExtractDefinitions(t *testing.T) {
 		"mixer/v1/attributes.proto",
 		"mixer/v1/config/client/client_config.proto",
 		"other/trailcomment.proto",
+		"other/full_references.proto",
 	}
 	for _, file := range testCases {
 		t.Run(file, func(t *testing.T) {
diff --git a/encoding/protobuf/testdata/full_references.proto.out.cue b/encoding/protobuf/testdata/full_references.proto.out.cue
new file mode 100644
index 000000000..a1f947941
--- /dev/null
+++ b/encoding/protobuf/testdata/full_references.proto.out.cue
@@ -0,0 +1,13 @@
+package full_references
+
+#FullReferenceMsg: {
+	nestedMsg?: #FullReferenceNestedMsg @protobuf(1,istio.io.api.other.full_references.FullReferenceNestedMsg,name=nested_msg)
+}
+
+#FullReferenceNestedMsg: {
+
+	#FullReferenceDoubleNestedMsg: {
+		value?: string @protobuf(1,string)
+	}
+	nestedMsg?: #FullReferenceNestedMsg.#FullReferenceDoubleNestedMsg @protobuf(1,istio.io.api.other.full_references.FullReferenceNestedMsg.FullReferenceDoubleNestedMsg,name=nested_msg)
+}
diff --git a/encoding/protobuf/testdata/istio.io/api/other/full_references.proto b/encoding/protobuf/testdata/istio.io/api/other/full_references.proto
new file mode 100644
index 000000000..2c81bde5d
--- /dev/null
+++ b/encoding/protobuf/testdata/istio.io/api/other/full_references.proto
@@ -0,0 +1,15 @@
+syntax = "proto3";
+
+package istio.io.api.other.full_references;
+
+message FullReferenceMsg {
+  istio.io.api.other.full_references.FullReferenceNestedMsg nested_msg = 1;
+}
+
+message FullReferenceNestedMsg {
+  message FullReferenceDoubleNestedMsg {
+    string value = 1;
+  }
+
+  istio.io.api.other.full_references.FullReferenceNestedMsg.FullReferenceDoubleNestedMsg nested_msg = 1;
+}