Graphic new video footage from northeastern Nigeria shows the country's military carrying out abuses against civilians as part of their fight against the armed group Boko Haram, human rights group Amnesty International has said.

One video, obtained by Amnesty and released on Tuesday, shows what appear to be military personnel and civilian vigilantes calling five detainees out from a row of 16 young men and boys, then slitting their throats one by one before dumping their bodies into an open grave.

The violence against civilians constitutes "war crimes," Amnesty alleged.

Amnesty said it obtained the footage from "numerous sources" in Borno state, Boko Haram's birthplace and stronghold.

The rights group said it independently confirmed from several military sources that the armed captors in the footage "were indeed military personnel."

Amnesty also accused the military of killing prisoners.

Some of the footage was apparently taken on March 14, the same day that Boko Haram broke into a military detention centre in Giwa barracks, freeing hundreds of prisoners. Amnesty says the military recaptured more than 600 of these prisoners and killed them.

The Nigerian military is studying the video footage "with a view to identifying those behind such acts," Defence Headquarters spokesman, Chris Olukolade, said in an email.

He added there will be "legal action against any personnel or anyone found culpable."

Nigerian authorities have rejected past accusations, insisting the military follows international best practice in its fight against the group.

More than 4,000 people - mostly civilians - have been killed this year alone "by all sides" of the conflict, said Amnesty.