The 'Bad Girls' musician was seen to raise her middle finger to the camera moments before a cutaway as she joined Nicki Minaj and Madonna on stage for a performance of 'Give Me All Your Luvin''.
"The NFL hired the talent and produced the halftime show," NBC said in a statement. "Our system was late to obscure the inappropriate gesture and we apologise to our viewers."
A number of Twitter viewers reported that their screens had blurred briefly during the halftime show, speculating that it may have been to censor part of the performance.
The NFL added in its own statement that MIA had not done anything similar during rehearsals and it did not believe that she would make such a gesture during the live show.
"The obscene gesture in the performance was completely inappropriate, very disappointing, and we apologise to our fans," said spokesperson Brian McCarthy.
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Watch Madonna's Super Bowl half-time show below:
See a gallery of the performance below: