NIGERIA'S emergency agency has denied a report from one of its officials that 15 people were killed at a church in the country's volatile northeast, saying two were dead in unclear circumstances.

An official from the National Emergency Management Agency (NEMA) on Monday told reporters that attackers had killed 15 people during a church service on Sunday in a remote village outside the town of Chibok.

The official who spoke is the agency's co-ordinator for the northeast region, but the agency's headquarters issued a statement on Tuesday providing a drastically different version. The military meanwhile denied any incident occurred.

The statement said the emergency agency had contacted the official quoted, Mohammed Kanar, and he had denied giving the information.

NEMA "has denied a report claiming that 15 worshippers were killed in an outskirt of Chibok local government council of Borno state on Sunday", the statement said.

"Though some of the reports claimed a source from NEMA provided the information, the agency not only contacted the same officer who denied it in its entirety, it also assigned a special team to investigate and verify the allegation which was later found to be unsubstantiated and untrue.

"Meanwhile the team has also discovered that two people were killed by unidentified gunmen around the area on Sunday and whose bodies had been deposited in a hospital. The victims were a security man and a bystander."

Lieutenant Colonel Sagir Musa, a spokesman for a military task force in the region, which has been hard hit by Islamist extremist group Boko Haram, told AFP he was not aware of any incident in the area on Sunday.

Asked about the NEMA statement saying two were dead, he maintained his previous statement and declined further comment.

Death tolls and information on attacks are often controversial and conflicting in Nigeria, with authorities under pressure to show progress in the fight against Boko Haram.