Jerry Omodara said it was not clear where the vessel had been taken to and efforts were being made to track it.
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.
Analysts say piracy is increasing in parts of West Africa.
In the first six month of this year, the International Maritime Bureau says it has recorded 17 pirate attacks in Nigerian waters this year - a significant increase on 2011.
The IMB told AFP the tanker was hijacked late on Tuesday from the port in Lagos.
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.
Lt Commander Omodara said a helicopter and two navy ships were trying to locate and rescue the tanker.
Last year, Nigeria and neighbouring Benin began joint naval patrols in an effort to combat the threat of pirates.
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