Amnesty International says there is sufficient evidence for the International Criminal Court to probe senior Nigerian military officers for war crimes in the battle against Boko Haram.

But Nigeria's military has accused Amnesty of publishing a "biased and concocted report" to discredit the country and its efforts to defeat extremism.

Amnesty on Wednesday stated the case against five senior officers in a new 133-page report based on hundreds of interviews, including with military sources, and using leaked defence ministry documents.

Amnesty's Secretary General Salil Shetty described the evidence of abuses collected as "sickening".

"In the course of security operations against Boko Haram in northeast Nigeria, Nigerian military forces have extrajudicially executed more than 1200 people; they have arbitrarily arrested at least 20,000 people, mostly young men and boys," the report said.

Nigerian forces "have committed countless acts of torture; hundreds, if not thousands, of Nigerians have become victims of enforced disappearance; and at least 7000 people have died in military detention as a result of starvation, extreme overcrowding and denial of medical assistance", it added.

Amnesty said commanders based in the northeast "should be investigated for potential responsibility for war crimes of murder, enforced disappearances and torture".

Top service chiefs in the capital Abuja should also be investigated given "they should have known about the commission of the crimes, and failed to take adequate action".

The ICC previously opened a preliminary investigation into the Boko Haram conflict but its tribunal stated there was insufficient evidence tying Nigeria's military to orchestrated atrocities targeting civilians.

But Amnesty said the evidence in its new report was sufficient to reopen the issue.

New President Muhammadu Buhari has pledged to improve systems so disciplinary steps are taken against proven human right violations by the armed forces.

But on Wednesday Nigerian defence spokesman Chris Olukolade accused Amnesty of publishing a "biased and concocted report" to discredit the country and its efforts to defeat Boko Haram.

"The officers mentioned in the report have no reason whatsoever to indulge in the allegation made against them," he said in an emailed statement.

Olukolade rejected claims the military and government had failed to respond to previous allegations of abuses and said detention facilities had been opened up to rights bodies and other groups.

"So far no allegation has been sufficiently proved against those whom Amnesty International is so desperate to convict, Olukolade added.