Cookson, who has been president of British Cycling since 1996, also promised a thorough investigation into allegations the UCI helped cover up doping would be completed within the first six months of his presidency.
The 62-year-old has based his candidacy on restoring trust and credibility in the UCI as the Swiss-based organisation struggles to deal with the aftermath of the Lance Armstrong doping scandal and allegations it did not do enough to catch the American, stripped of his seven Tour de France titles last year.
"The most important challenge for the next president is to address the way cycling deals with doping," Cookson told a news conference in Paris on Monday.
"The reality is that the UCI is not trusted, our anti-doping is not seen to be independent and we don't have the trust of the World Anti-doping Agency (WADA) and the other key anti-doping agencies.
"At the moment, the anti-doping service within the UCI headquarters is just down the corridor of the president's office so that can't be right," Cookson added.
"If elected president, I would rapidly establish a completely independent anti-doping unit, in cooperation with WADA. It will be managed and governed outside of the UCI so people can have absolute confidence in our sport."
While saying that several international federations have already set up "outsourced" anti-doping units, Cookson did not elaborate further on his plan.
Cookson also said he would try and improve the UCI's rocky relationship with WADA.
"It's absurd that a sport that has suffered so much from doping has been in open conflict with the very people it should be working with," he said.
In January, the UCI disbanded its own independent commission set up to look into the accusations made against the governing body concerning the Armstrong scandal in favour of a "truth and reconciliation process" with WADA that has still to be launched.
The move stirred another row between the two institutions, with WADA saying they had not been consulted.
Cookson, who has been a member of the UCI's management committee for four years, is challenging incumbent Pat McQuaid, running for a third term as president, in the September elections.