The Football Association have asked Fifa to clarify what rules Arsenal might have broken regarding their relationship with Belgian club Beveren.
Arsenal say they do not have control of any other clubs
Fifa want the FA to look into claims they made payments to Beveren.
FA spokesman Mark Hooper said: "We will await clarification on whether the allegations breach Fifa rules."
Premier League rules prohibit clubs making loans or owning shares but these rules do not apply to dealings with a club based outside of England.
A Belgian police inquiry discovered secret money links between Arsenal and Beveren to fund the club's takeover.
But Beveren club spokesman Dirk Dobbeleir said: "We have nothing to fear.
"A joint venture agreement has been made between Arsenal and Beveren but the police said everything was in order and there was no case to answer.
"We don't know why the media suddenly made so much of the matter though probably because the name Arsenal made it newsworthy."
Fifa communications director Markus Siegler said: "According to the structure of rules which are in place, the FA have to look into the matter.
"Fifa are interested in all cases around the world but individual members must run football in their country.
"They must take responsibility for their members so absolutely this is a case for the FA to deal with."
If found guility, Arsenal could be punished with anything from a fine to being relegated from the Premiership or kicked out of the Champions League.
The investigation, which was shown in a television report on Newsnight on Thursday, suggested that Arsenal had used Belgium's slack rules to recruit players from Africa.
The Gunners signed Emmanuel Eboue from Beveren for £1.5m.
While the FA have been instructed to lead the investigation, leading sports lawyer Mel Goldberg does not think Arsenal have anything to fear.
Goldberg told Five Live Sport: "Uefa and Fifa have rules about clubs owning shares in foreign teams.
"I don't think that's happened here because Arsenal say, rightly, they have no control of a foreign club."
Goldberg added: "There are two sets of rules you need to look at.
"One is the Premier League rules which prevent clubs owning shares or an interest in another Premiership or Football League club. That hasn't happened here.
"Then there are Uefa and Fifa rules which are similar, about clubs owning shares in foreign teams, and I don't think that's happened either."
The Belgian police investigation forced Arsenal to admit they had indirectly loaned Beveren £1m, although previously they had denied putting any money into the club.
A statement from the Gunners said: "Arsenal confirms it has never owned, directly or indirectly, any shares in Beveren or had any power whatsoever to influence its management or administration."