diff --git a/scene/2d/navigation/navigation_agent_2d.cpp b/scene/2d/navigation/navigation_agent_2d.cpp
index 8fd09e90d79..d8c8abece6b 100644
--- a/scene/2d/navigation/navigation_agent_2d.cpp
+++ b/scene/2d/navigation/navigation_agent_2d.cpp
@@ -416,7 +416,9 @@ void NavigationAgent2D::set_navigation_layers(uint32_t p_navigation_layers) {
 
 	navigation_layers = p_navigation_layers;
 
-	_request_repath();
+	if (target_position_submitted) {
+		_request_repath();
+	}
 }
 
 uint32_t NavigationAgent2D::get_navigation_layers() const {
@@ -535,7 +537,9 @@ void NavigationAgent2D::set_navigation_map(RID p_navigation_map) {
 	map_override = p_navigation_map;
 
 	NavigationServer2D::get_singleton()->agent_set_map(agent, map_override);
-	_request_repath();
+	if (target_position_submitted) {
+		_request_repath();
+	}
 }
 
 RID NavigationAgent2D::get_navigation_map() const {
diff --git a/scene/3d/navigation/navigation_agent_3d.cpp b/scene/3d/navigation/navigation_agent_3d.cpp
index 3b4c55ca38b..83faf29150b 100644
--- a/scene/3d/navigation/navigation_agent_3d.cpp
+++ b/scene/3d/navigation/navigation_agent_3d.cpp
@@ -453,7 +453,9 @@ void NavigationAgent3D::set_navigation_layers(uint32_t p_navigation_layers) {
 
 	navigation_layers = p_navigation_layers;
 
-	_request_repath();
+	if (target_position_submitted) {
+		_request_repath();
+	}
 }
 
 uint32_t NavigationAgent3D::get_navigation_layers() const {
@@ -572,7 +574,9 @@ void NavigationAgent3D::set_navigation_map(RID p_navigation_map) {
 	map_override = p_navigation_map;
 
 	NavigationServer3D::get_singleton()->agent_set_map(agent, map_override);
-	_request_repath();
+	if (target_position_submitted) {
+		_request_repath();
+	}
 }
 
 RID NavigationAgent3D::get_navigation_map() const {