The game, which ended 1-0 in favour of visitors Chelsea at Baba Yara Sports Stadium, was halted for a while 10 minutes to full-time as home supporters hurled missiles onto the pitch in protest of a refereeing decision.
There was even more trouble after the match as the angry fans sought to attack the referee, provoking a clash with local police and leading to serious injuries.
"The Ghana Football Association has learnt with extreme disappointment the unfortunate incidents at the Baba Yara Stadium in Kumasi during the Ghana Premier League match between Asante Kotoko and Berekum Chelsea on Sunday," the GFA said in a statement on its official website on Sunday night.
"We are saddened by reports of injuries to football fans and the hospitalization of a fan, following an alleged gun shooting incident.
"Our profound sympathy goes to the injured, and we pray for speedy recovery.
"The Ghana Football Association takes a dim view of violence at all league centres across the country and totally condemns what may have precipitated the unfortunate development at the Baba Yara Stadium."
Reports indicate violence broke out after Kotoko centre-back Empem Dacosta was sent off for a second bookable offence. The Porcupine Warriors protested the second yellow card, insisting the foul was instead committed by midfielder Kwame Adom.
After the game, the clash continued, leading to some injuries. A Kotoko fan suffered a bullet wound and was rushed to the Komfo Anokye Teaching Hospital.
"While we conduct our own inquest from our designated matchday officials to find out the exact cause of the unfortunate incidents, we call on the Police Service to also conduct a thorough investigation, especially on the alleged shooting incident," the statement continued.
"The GFA wishes to assure the general public that it has zero-tolerance for violence, and in accordance with our regulations, will deal ruthlessly with any official or club that is found to have breached our GFA Regulations and GFA Disciplinary Code.
"Once again, we wish the injured speedy recovery."
Kofi Owusu scored the lone goal on the day, denying the Porcupine Warriors three points for the first time this season.