Senegal launched a complaint after Sakho played in the Hammers’ FA Cup clash with Bristol City on January 25 despite missing the Africa Cup of Nations with a back injury.
The Premier League club maintain correct procedures were followed, but in the wake of the dispute subsequently decided to leave Sakho out of the squad for Saturday’s match at Liverpool, which they lost 2-0.
A FIFA statement on Monday morning said: “We can confirm, that disciplinary proceedings were initiated against the player Diafra Sakho (SEN) and the club West Ham United for a potential violation of the FIFA Regulations on the Status and Transfer of Players.
“At this stage we can’t make any further comments.”
Should the case be proven then Sakho could face a domestic suspension and West Ham a fine from the world’s governing body.
It has also been suggested West Ham could face a compensation claim from Bristol City should FIFA rule they fielded a player who should have been ineligible.
Hammers manager Sam Allardyce had defended the decision to play Sakho at Ashton Gate, the forward having been driven down from London owing to medical advice barring him from travelling by plane.
However, the club later decided not to select him for the Premier League match at Anfield.
Speaking on Saturday, Allardyce confirmed: “With Sakho it is down to the situation we are in with FIFA. While it is happening it is not conducive for us to be putting him on the field until it is resolved sadly.
“If you speak to the lad you would know how angry and disappointed he is at being denied the opportunity to play football when it is not our fault.
“We have covered all the rules and regulations, but at this moment in time it is sensible to do the right thing and not get involved any more.”