Group F is set to get under way on September 13 with Benfica due to travel to Denmark to face FC Copenhagen on the same night as the Scottish champions visit Old Trafford.
However, Portuguese minnows Gil Vicente have taken legal action against their football association (FPF) after being relegated last season for gaining eligibility for a player - Angola international Mateus - at a civil court.
FIFA have given the FPF a deadline of September 14 to resolve the situation or face disciplinary action, which could see a ban being imposed on Portugal's national team and clubs.
Benfica could be banned from the Champions League, leaving possibly just three teams competing for the two top places and a place in the money-spinning knock-out stages.
A FIFA spokesman told PA Sport: "There is a possibility of this existing.
"There is an issue in Portugal with the club Gil Vicente, who are in dispute with the Portuguese Football Association.
"Because of this we have asked the Portuguese Football Association to solve the problem internally or with the sporting governing bodies.
"They have until September 14 to resolve the matter but after the deadline we would submit the case to the emergency committee and they would review the matter.
"A ban is an option and when a federation is banned there are no international matches to be played by that nation and the clubs so that would affect the Champions League."
UEFA have also admitted Porto, who are in Arsenal's group, and Sporting Lisbon could be excluded from the Champions League.
European football's governing body have been looking at which teams could be drafted in as replacements but the timing of FIFA's action may leave them with no option but to have just three teams in Group F and three in Group G.
A UEFA spokesman told the Daily Record: "If FIFA decide to ban the Portuguese FA and its clubs then that will obviously have an impact on our competition.
"But it is only at that point we would have a look to see what else UEFA could do.
"For instance, as one of the options, we would have to decide whether or not to play the group with just three teams." Tweet

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In reallity teams are rarely thown out. I would bet that it will all be sorted out by the 14th with the portuguese teams still being in the CL.
If we cannot get past Benfica again this year then why should we think that we are going to win the CL?
If there's a ban it should be next season not this.Let's play it fair the draw has been made and Celtic and UNITED and Copenhagen will have made preparations,and expect to play.
Ban them all !!!!! Then ban clubs in the last 16, 8 and we may win this season with Fletcher as captain.
Ban Fergie ! Fergie out !!
If we need clubs banned to get through the group then we dont deserve to be in the tournament at all. Players should desire to prove themselves at the highest levels by playing against the best, not by srapping through due to the misfortunes of others
United would only have to avoid last place in the group to secure qualification. Something that has proven beyond them just recently.
Pathetic! No bans are necessary. I want to play Benfica, a bit of revenge the right way!
Manc, Abroad. Thanks for the inteligent comment on the story. The Fletcher haters really need to get a grip. This kid is playing his guts out for the team and all they can do is swill down their pints and type out the same old rubbish thread after thread. Grow up.
The ban will never happen at this stage of the tournament because of something called a law suit.
I suppose you'll understand that Rio will want a pay rise because of this? He was hoping to go there with Man U but will now have to pay out of his pittance to go there on his hols!
Ban them all & give us their prize money. It amounts to about 48million & will ALMOST make up the shortfall on this year's interest payments.
We will get through, Benfica or not.
Pathetic, have we reached such a low level in Europe that we need help from UEFA banning Portugese clubs.
Being the No.1 in Europe is all about beating the best teams and, for the fans, going to the great European nights at OT playing Real Madrid, Barca, Milan, Juve etc. etc.
As someone who loves football I,m always pleased and delighted when the top teams play and the best team is the champion. If it so happens that Man Utd are not good enough to win then the next best thing is the best and most attractive team, like Barca last season.
I totally disagree... When I saw the draw for this group, I thought it was perfect as it gives us a chance to banish the ghosts of last season.. I say, don't ban them, let us have our due revenge..
Can Someone Please Put A Comment down Saying How Much Prize Money You Get From The UEFA Champions League Please I Really Need To Know Or Put Down A Website That Could Tell Me!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
john in glasgow; you are spot on; the italian fiasco shows that football in europe rarely sorts out its own house; come the day benfica will be in. United will walk the group anyway!!
About 2 quid Man Utd fan, Australia...
United haven't made this statement you great numptys, why do you keep on banging on about how low we have stooped to have to rely on Benfica getting booted? we don't have to rely on Benfica getting booted, I am happier if Benfica do stay in the competition because we have an opportunity to really banish the ghost of last season and stick it to them.