It is alleged the club's manager placed bets with at least three of its French international players on the outcome of the Scotland vs France game and the reverse fixture in the Euro 2008 qualifying campaign at the end of last year.
The Football Association does not allow any player, coach or official to gamble on matches they are involved in.
Although Ferguson himself has not broken any rules, as he was not involved in the Scotland/France matches, two French stars - Patrice Evra and Louis Saha - could face action.It is also claimed Ferguson placed bets with French player Mikael Silvestre - but he did not play any role in either of the games.
Saha came on as a sub in the 62nd minute during the Scotland v France game on Saturday, 6 October, 2006, at Hamden Park, Glasgow.
Evra was in the squad but not did not make it on to the substitute bench.
Scotland won the game 1-0 thanks to a Gary Caldwell goal in the 67th minute.
In the second game on 12 September, 2007, at the Parc des Princess, Paris, Evra was on the substitute bench but was not brought on so did not play.
Saha was in squad but did not make it on to the team sheet that day.
The FA confirmed it will launch an investigation into the United betting allegations, which appeared in an article about Man United's Scottish international player Darren Fletcher in this week's Zoo magazine.
They are also alerting Fifa and Uefa to the matter.
An FA spokesman said: "We will take action against any participants in our leagues found to be in breach of our regulations, if it is proved they bet on a match that they were involved in or could potentially influence.
"In general terms, no one in the Premiership can make bets on games they are involved in, in any way."
He added: "The comments in question seem to suggest that several Manchester United players made bets with Sir Alex Ferguson on an international match they were playing in, contravening those rules.
"We will be fully investigating the quotes made by Darren Fletcher but this matter may also be highlighted to FIFA, as the games in question were international matches, and Uefa as the tournament organisers.
"It's something we are going to have to look very closely at but we can only take action against players who break the rules of the matches and competitions under our jurisdiction."
In an interview in Zoo magazine, United star Fletcher said: "He [Ferguson] was happy when Scotland beat France. He won a bit of money because he was making bets with all the French lads - Patrice Evra, Louis Saha and Mikael Silvestre.
"They were looking at him like he was a bit crazy, so they took any bet.
"But he had the last laugh 'cos we managed to beat them twice!"
Ferguson and the United squad were celebrating today after winning their crucial European Champions League semi-final second leg against Barcelona at Old Trafford.
The win means it will be the first ever all English Champions League final.