Following a two-month inspection, it said most of them have been taken over to hawk stuff and do other business.
Some stink or are in disrepair, others lack information boards or are hidden by trees, it said.
The Department blamed the Public Transport Management and Operation Center, which is entrusted with managing the bus stops.
Chief inspector Le Vinh Phat said the Center does not check them regularly and so does not discover the problems in time.
But the Center said it does not have adequate funds for the task.
The Department’s director has asked the center for details of its spending on maintenance of the bus stops last year and the reasons for the problems listed by the inspectors.