The NAF suggested that the accident was due to an air crash.
The video was published by SITE Intelligence Group and is circulating in the Nigerian media.
“It is evident that many parts of the video were deliberately altered to give the false impression that the aircraft was shot down” when it was “obviously an air crash,” said NAF in a statement posted on Facebook on Friday.
NAF rejected the seven-and-a-half-minute clip, calling it “false propaganda” and urging Nigerians “to ignore the content of the videos circulating until all investigations into how the aircraft crashed are completed”.
NAF reported the plane’s disappearance on Wednesday, with two pilots on board.
A spokesman told CNN on Thursday afternoon that the jet fighter was deployed near Borno state, in northeastern Nigeria, to provide air support to ground troops, who were under fire from Boko Haram fighters before radar contact was lost.
“The cause of the accident, as well as the whereabouts of the 2 pilots, remain unknown. The pilots are flight lieutenant John Abolarinwa and flight lieutenant Ebiakpo Chapele,” said NAF on Friday.
In the disputed video, Boko Haram claims to have dropped the Alpha Jet.
The footage shows several fighters shooting into the air before an explosion lights up the sky when an airplane catches fire and falls to the ground. The video cuts to the fighters standing around what appears to be the wreckage of the jet.
Then it cuts to the plane, showing “NAF 475” – the missing aircraft’s identification number. Later, it shows a charred body.
Separately, the video shows what appears to be a patch on the floor, displaying the name of John Abolarinwa.
CNN cannot independently verify the authenticity of the video.
Boko Haram has stepped up attacks against the Nigerian military in an attempt to regain control of territories lost in pockets in the northeast of the country.
The frequent air strikes by the Nigerian military continued to shake up insurgents – dislodging them from their hiding places.