The current English, European and World champions sported a special emblem in the centre of their shirts during their Champions League last 16 encounter on Wednesday night, acknowledging their status as the best team in the world following their Club World Cup success in Japan in December.
However, the Old Trafford outfit have now been told by Soho Square that they will not be allowed to wear the motif in Premier League matches.
Instead, they will only be permitted to sport the crest in FA Cup ties until December when a new Club World Cup champion is crowned, unless United successfully defend the title.
FIFA President, Sepp Blatter was present at Old Trafford on Wednesday, presenting United chief executive David Gill with the crest.
"Manchester United have won a multitude of honours during their illustrious history but in Tokyo last December they added a new title, that of FIFA World Club champions," he said.
"This commemorative presentation recognises the achievement of Sir Alex Ferguson and his players and means that until late December 2009, every time the team takes to the field, they will take that honour with them on their shirts."
Blatter is due to meet Premier League chief executive Richard Scudamore in Zurich next week, where the matter is expected to be debated, along with FIFA's controversial six-plus-five player quota scheme.
"It makes more sense for Manchester United to wear the badge in every game in every competition, rather than just in the Champions League," added FIFA Secretary General Jerome Valcke. "That is what Milan did for all of last year while they were entitled to wear it.
"But the FA Premier League has to be different. Their view is that it should only be worn in the Champions League as that is the competition which you have to win to enter the Club World Championship.
"But you could say that you have to win the Premier League to be in the Champions League."
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