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Assisting individuals in their daily activities through autonomous mobile robots, especially for users without specialized knowledge, is crucial. Specifically, the capability of robots to navigate to destinations based on human speech instructions is essential. While robots can take different paths to the same goal, the shortest path is not always the best. A preferred approach is to accommodate waypoint specifications flexibly, planning an improved alternative path, even with detours. Additionally, robots require real-time inference capabilities. This study aimed to realize a hierarchical spatial representation using a topometric semantic map and path planning with speech instructions, including waypoints. This paper presents Spatial Concept-based Topometric Semantic Mapping for Hierarchical Path Planning (SpCoTMHP), integrating place connectivity. This approach offers a novel integrated probabilistic generative model and fast approximate inference across hierarchy levels. A formulation based on control as probabilistic inference theoretically supports the proposed path planning algorithm. We conducted experiments in home environments using the Toyota Human Support Robot on the SIGVerse simulator and in a lab-office environment with the real robot, Albert. Users issued speech commands specifying the waypoint and goal, such as "Go to the bedroom via the corridor." Navigation experiments using speech instructions with a waypoint demonstrated a performance improvement of SpCoTMHP over the baseline hierarchical path planning method with heuristic path costs (HPP-I), in terms of the weighted success rate at which the robot reaches the closest target and passes the correct waypoints, by 0.590. The computation time was significantly accelerated by 7.14 seconds with SpCoTMHP compared to baseline HPP-I in advanced tasks.