Nicholas Mensah joined the defending champions at the beginning of the season on a three-year deal from Delsanco FC.
However, a protest was filed against him by title rivals Aduana Stars after a scoreless draw between the two sides in the 10th round of matches.
Aduana requested that the GFA charge Kotoko for name inconsistencies regarding the player, but Kotoko was found to be innocent in the matter.
Despite being cleared, Kotoko have taken the decision to deal with possible violations based on the advice of the Disciplinary Committee.
“Aduana FC filed a protest against Asante Kotoko SC for fielding an unqualified player in the person of Nicholas Mensah after our match day 10 encounter,” Kotoko’s statement read.
“The protest case has been determined and duly dismissed. However, the registration of Nicholas Mensah has been suspended due to infractions which according to the Disciplinary Committee occurred prior to him joining Asante Kotoko.
“Our legal team is dealing with the matter and would take the necessary steps to assist the player.
“Nicholas will be given the necessary psychological help throughout this debacle.”
The 20-year-old is the second top scorer for Kotoko this season in the Ghana Premier League with three goals after Stephen Mukwala who has eight goals.