The International Cycling Union (UCI) made a mistake accepting a donation from Lance Armstrong in 2002, president Pat McQuaid has admitted.
In 2012 Armstrong, 41, was banned for life and stripped of seven Tour de France titles for serial doping.
The UCI received $125,000 from the American in 2002, but said in 2010 that this was not part of a cover-up.
"On reflection, it would have been better had we not taken that money," McQuaid, 63, told BBC Radio 5 live.
The Irishman, who is seeking re-election as UCI president, added: "Having said that, when we took it, we announced publicly, with a press statement, that the money was being given and what the money was being used for.
"It was done with the best interests, not in any underhand way."
Armstrong received a life ban from the United States Anti-Doping Agency for what it called "the most sophisticated, professionalised and successful doping programme that sport has ever seen".
The UCI denied it accepted the money to cover up a positive drug test from Armstrong.
McQuaid, who is opposed for the UCI leadership by head of British Cycling Brian Cookson, also believes the UCI is a victim of its own success in catching cheats.
"When we catch cheats, it's used in a sense as a stick to beat the back of the UCI and I think that's a little bit unfair," he said.
"We spend in the region of seven million Swiss Francs (£4.87m) a year to catch cheats.
"You don't spend that sort of money and fail. You don't spend that sort of money and not want to catch cheats."