The Ghanaian club hosted TP Mazembe of the DR Congo in Accra on Sunday and won 1-0 even though they could not qualify for the semi-finals.
The result left the visitors with a daunting semi-final against defending champions Esperance of Tunisia.
A Tunisian news report had claimed that TP Mazembe officials offered to bribe Berekum Chelsea to give the Congolese side an easier semi-final.
Victory for TP Mazembe would have seen them top the group and play Sunshine Stars of Nigeria.
In a statement on Monday, Berekum chief executive Nana Kwame Nketiah said there was no meeting with anyone from TP Mazembe.
"We have not met any TP Mazembe official or officials, let alone discuss the issuance of bribes or anything thereof," the statement said.
It went on: "We want to assure all Ghanaians, Berekum Chelsea fans and members African football fraternity that we will not desecrate the sanctity of our club and African football with such dubious acts."
Nketiah has threatened to take legal action.
Ghana Football Association chairman Kwesi Nyantakyi, who was at the game, also took a swipe at the allegation.
"It damages the integrity of the clubs," said Nyantakyi, who is also on the Confederation of African Football's executive committee.