The area around the blast has been sealed offThe explosion happened in the Mammy market, where soldiers and civilians gathered to eat and drink beer celebrating New Year's Eve.
Air Marshal Oluseyi Petirin blamed "devilish people" but did not name any group or give a possible motive.
He also declined to give any casualty figures.
State TV has said 30 people were killed but other sources say four people have died.
Witnesses have told the BBC they saw body parts lying on the ground and injured people being carried away after the blast.
"People ran in different directions. There were scores of bodies - dead and wounded. They used army trucks to pack them away," a market regular called Eric said, reports the Reuters news agency.
Air Marshal Petirin said a bomb had been placed "where people were relaxing and generally being happy because of the New Year which is approaching".
He urged Nigerians to be vigilant following a recent spate of bomb attacks in a country where they had been almost unknown.
"Do not allow anybody to come and leave a bag, or any kind of object, especially when he is not there," he told state TV.
The market is near the Sani Abacha barracks, named after Nigeria's late military dictator, in Asokoro district, home to the presidential palace and said to be the city's most secure area.
Officially renamed the Mogadishu Cantonment, the barracks is still known to many by its old name.
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