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.
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."
"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."