Fifa has written to the Football Association requesting it investigates the relationship between Arsenal and Belgium club Beveren.
The BBC's Newsnight programme claims the Gunners made payments to Beveren.
The letter said: "We kindly ask you to carry out an investigation into the relevant relationship between your affiliated club, Arsenal, and Beveren.
"We would be grateful to be updated on the developments and informed of the findings as soon as possible."
The statement added: "We ask you to carry out an investigation to ensure proper clarification of the issue."
Newsnight learned that a police probe in Belgium had concluded Arsenal made secret payments of £1m to Beveren.
Arsenal have admitted providing a loan to Beveren indirectly, but say they have never had a controlling influence over the Belgian club.
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.
The Gunners have an arrangement with the Belgium club to play friendly matches and loan players.
Arsenal deny allegations of making irregular financial payments to Beveren.
An FA spokesman said: "We have received Fifa's letter asking us to carry out an appropriate investigation into the allegations relating to Arsenal.
"As requested our compliance department will be in contact with Arsenal regarding this matter."