The Football Association has announced that it has not uncovered any evidence of wrongdoing by Arsenal in the club's relationship with Belgian side Beveren.
BBC Newsnight said Belgian police found that Arsenal made irregular payments to Beveren, charges the club denied.
Football's world governing body Fifa asked the FA to investigate, but it concluded the Gunners had not breached any FA or Premier League rules.
The material obtained during the FA's investigation has been sent to Fifa.
"As a result of our inquiries, we can confirm that we have not identified any evidence to suggest that Arsenal have breached any rules of the FA or the FA Premier League (FAPL) in relation to their dealings with Beveren," read an FA statement.
"In order to protect the integrity of matches and competitions, these rules prohibit clubs in the same competition from being owned, influenced or controlled by the same person or entity.
The FA has established that Beveren is a Belgian football club and therefore does not compete against Arsenal in the Premiership or the FA Cup. This is not what Sepp Blatter asked for
The Football Association has undertaken a thorough and appropriate inquiry
"In this case, the relevant competitions are the FA Cup and the FA Premier League. The rules also prevent a Premier League club from owning or controlling another Premier League or Football League club."
Newsnight responded to the announcement by saying: "After its investigation the Football Association has concluded that because Beveren is a Belgian football club, there is no evidence that Arsenal has breached any of its own FA or FAPL rules.
"But this is not what Sepp Blatter asked it to investigate.
"The FA has not investigated any of the allegations in the original Newsnight film which related to dealings between Arsenal, Beveren and the Ivory Coast."
However an FA spokesman insisted: "We have conducted an inquiry in line with their request.
"The FA has undertaken a thorough and appropriate inquiry and will continue to offer any assistance that Fifa may require."
Newsnight revealed on 1 June how Belgian police uncovered an investment into Beveren of £1m from an anonymous donor, which they subsequently concluded had been provided by Arsenal.
Arsenal admitted providing a loan to Beveren indirectly, but said 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.
Ivory Coast defender Emmanuel Eboue moved to Arsenal following a successful spell with the Belgian team.