It is unclear what sparked the clashes but a senior police officer told the BBC that a police station had been set on fire.
One media report says that a policeman had confronted a navy officer for failing to stop at some traffic lights.
The police and the navy have not officially commented on the incident.
Images of burned cars and building were shared on the Nigeria police Facebook page but they have since been removed.
Another media report says that a navy officer who had been involved in a minor accident with a motorised rickshaw had been angered by the policeman's behaviour.
Shortly afterwards, a group of armed naval officers are said to have attacked and burnt down a local police station.
The BBC's Martin Patience in Lagos says the attack highlights the often lawless behaviour of the country's defence forces.