The NAF suggested that the accident was due to an air crash.
The video was published by the SITE Intelligence Group and distributed in Nigerian media.
“It is clear that most parts of the video were deliberately doctored to give the false impression that the plane was shot down” when it ‘was apparently an air crash,’ the NAF said in a statement on Facebook.
The NAF rejected the seven-and-a-half-minute edited clip, calling it “false propaganda” and urging Nigerians “to ignore the contents of the videos that make the rounds until all investigations into the crash of the plane have been completed.”
The NAF reported the plane missing on Wednesday, with two pilots on board.
A spokesman told CNN on Thursday afternoon that the fighter jet was deployed near Borno State in northeastern Nigeria to provide air support to ground troops, who were under fire by Boko Haram fighters before losing radar contact.
“The cause of the crash as well as the location of the two pilots is unknown. The pilots are Lieutenant John Abolarinwa and Lieutenant Ebiakpo Chapele,” the NAF said earlier Friday.
In the disputed video, Boko Haram claims to have shot down the Alpha Jet.
The footage shows several fighters firing into the air before an explosion ignites the air as a plane catches fire and falls to the ground. The video then cuts to fighters standing around the wreckage of the jet.
It then cuts to the plane, with ‘NAF 475’ – the missing plane’s ID number. It later shows a charred body.
Separately, the video then shows a patch on the ground showing John Abolarinwa’s name.
CNN cannot independently verify the authenticity of the video.
Boko Haram has stepped up attacks against the Nigerian army as it seeks to regain control of lost territory in the north-east of the country.
Regular airstrikes by the Nigerian army continued to rattle the insurgents and drive them out of their hiding places.