Navy spokesman Kabir Aliyu told the BBC the crew was safe, the hijackers had fled and the vessel, the Abu Dhabi Star, was being escorted into the port of Lagos.
Earlier, the navy denied reports that the tanker was seized in the port.
There has been a significant increase in the number of pirate attacks in parts of West Africa.
The BBC's Will Ross in Lagos says instead of seeking a hefty ransom the armed gangs tend to steal the cargo before releasing the crew.
The International Maritime Bureau (IMB) told the AFP news agency that 23 crew members were on board when the tanker was captured and they had locked themselves in a safe room.
Noel Choong, head of the IMB's Malaysia-based piracy reporting centre, said those behind the attack may be the same criminal syndicate that seized two tankers off Togo last month, siphoned off the oil and later released the crew and ships.
Last year, Nigeria and neighbouring Benin began joint naval patrols in an effort to combat the threat of pirates. Click to signup for FREE news updates, latest information and hottest gists everyday
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