The English champions sent their elite development squad to Croatia for the match but head coach Patrick Viera took his team off the pitch following allegations from Fofana that he had been subjected to racial abuse.
The midfielder made the complaint after he was sent off not long before half-time. It is understood that the move to remove the players from the pitcj was supported by City officials, while Vieira has also received the backing of anti-discrimination network FARE.
However, Rijeka have since issued a statement in which they dismiss the allegations strenuously. "Rijeka clearly and unequivocally rejects any possibility that the players at the match against Manchester City participated in assaulting the rival players on racial, religious or ethnic grounds," read a statement on the club's website.
"We want to point out the fact that we mentioned at the game we had six players from the Nigeria squad, players who live and train together with our other players, who learned the Croatian language and who have never experienced any discomfort by team-mates - as they themselves can attest.
"We also want to point out that Rijeka, in co-operation with FARE, supports a campaign against racism and strongly condemns any incident of its kind. Because of this, we are surprised by the unpleasantly harsh and baseless accusations of which we are accused."
Ranko Buketa, who was in charge of Rijeka's team on Tuesday, has also suggested that City simply wish to divert attention away from Fofana's actions which caused him to be sent off during the first half. "It looks like a move which is trying to hide a very ugly foul by the player that resulted in [a red card], followed by a hasty and illogical decision of the coaching staff to withdraw the team from the field," said Buketa.
It is not the first time that City's players have been involved in such ugly incidents. CSKA Moscow were ordered by UEFA to close part of their stadium after midfielder Yaya Toure was racially abused in a Champions League match in October. Porto were also fined £16,700 in 2012 after their supporters directed racist chants at Toure and striker Mario Balotelli, during a Europa League tie.
Youth team striker Devante Cole, son of former Manchester United forward Andy, was racially abused by players and fans during a youth match against Atletico Madrid, too.