A FIFA statement read: "Disciplinary proceedings were initiated against the player Diafra Sakho and the club West Ham United for a potential violation of the FIFA Regulations on the Status and Transfer of Players."
West Ham believe they will be vindicated in the dispute which began when the Premier League club said he could not travel to the tournament in Equatorial Guinea due to injury.
Senegal then made an official complaint to soccer's world governing body about him playing in the FA Cup fourth round for West Ham when he came off the bench to score in their 1-0 win at Bristol City last weekend.
Senegal, knocked out of the Nations Cup on Tuesday, remain angry that their officials were unable to examine Sakho themselves because West Ham said he was not fit enough to fly.
West Ham, however, have denied any wrongdoing with co-owner David Sullivan saying the club acted solely on the advice of leading medical professionals.
He said: "Any FIFA hearing will vindicate us, we have done nothing untoward."
Sakho was left out of West Ham's squad for this weekend's league match with manager Sam Allardyce explaining before the game at Liverpool: "It is not conducive for us to be putting him on the field until it is resolved, sadly.
"We have covered all the rules and regulations but at this moment it is sensible to do the right thing and not get involved any more.
"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."
Sakho has scored 10 goals in 16 appearances in all competitions since joining the Hammers from Metz before the start of the season.
