Nigerian troops have killed 20 suspected members of the armed group Boko Haram in the northeastern city of Maiduguri, the army says, an account quickly denied by the militant group.

Military commander Victor Ebhaleme said one soldier had been killed and two others injured in the raid on Sunday.

"We got a report that some suspected members of Boko Haram were meeting at a particular location in Maiduguri. Our men mobilised, leading to a shootout. Twenty suspected terrorists were killed," Ebhaleme told AFP news agency.

He said no arrests were made during the raid on the hideout in the Gwaidamgari area of Maiduguri, a hotbed of Boko Haram activity.

Boko Haram said on Sunday that none of its members had been killed, accusing the military of killing innocent people in an attempt to dislodge the group.

A spokesman for the group by the name Abul Qaqa, who has spoken to reporters on several occasions, said in a conference call that the claim by the military was false.

"They only succeeded in killing innocent civilians. It is not possible for 20 of our members to sit in a volatile place and hold (a) meeting," said Qaqa.

Maiduguri has been one of the targets of the group's deadly assaults, with scores of people killed in recent months.

The group wants to establish Islamic law in the country, whose large Christian and animist population mainly lives in the south.

Nigerian authorities have recently launched a military assault on suspected Boko Haram operational bases.

President Goodluck Jonathan said in June that Boko Haram was seeking to incite a religious crisis by attacking churches in an attempt to destabilise the government.

The US State Department last month designated three of the group's leaders as global terrorists.