Roland Djodji equalised for the Miners after Justice Blay had given Medeama an early lead but the referee awarded the hosts a late penalty which was converted by Kwesi Donsu.
After the final whistle, a furious Akonnor confronted the referee in the tunnel, according to reports.
“I was really shocked when I read that story. I am a professional [coach] and have been in this career for so long," Akonnor told Graphic Sports.
"I know how things work so why will I fight with a referee just because my team lost a match? In fact, it was one of the worst news reports I have read about myself and I want to distance myself from it.
"This is because it is never true that I attacked the referee since I was [even] standing far away from where the incident of misunderstanding happened,” he added.
Ashanti Gold recovered from that defeat to pip Techiman Eleven Wonders 1-0 on Wednesday and have opened up a three-point lead at the summit of the table.