The star-studded commercial, which carries the slogan 'Write The Future', premiered during ITV1's Champions League final coverage on May 22.
However, some viewers in Wales and the south of England missed the final six seconds of the ad, which focuses on the fame surrounding footballers such as Ronaldo, Wayne Rooney, Didier Drogba and Ronaldinho.
"A technical problem affected play-out of a Nike advertisement for approximately six seconds to ITV1 regions in the south of England and Wales," said an ITV spokesman.
"ITV has apologised unreservedly to Nike and we are engaged in dialogue with the client regarding the issue."
The final part of the ad features the slogan 'Write The Future', along with the Nike "swoosh". However, viewers in the affected areas just saw a static ITV1 logo.
Reacting to the transmission error, a Nike spokesman said: "We have had over 5m views of the 'Write The Future' film in the last four days on our YouTube channel alone, so we are confident that the fans knew what they were watching.
"Having said that, it is disappointing if ITV cut the ad before the end and we're waiting to hear back from them on exactly what happened."
It is thought that both parties are close to reaching a compensation deal for the error which will involve Nike receiving an undisclosed amount of airtime.