Cookson also said he wants former UCI leader Hein Verbruggen to give up his honorary presidency after the 227-page dossier said the governing body colluded with Lance Armstrong to cover up positive tests at the 1999 Tour de France.
The International Cycling Union was severely criticized in the report for failing to act during the doping era dominated by Armstrong, and broke rules to favour the now-disgraced rider.
The report was commissioned by the new UCI leadership to investigate doping that shredded cycling's credibility and led to Armstrong being stripped of his seven Tour de France titles in 2012.
While the yearlong probe turned up no major revelations, and found no proof that payments Armstrong made to the UCI was to cover up positive tests, it suggested doping is still rife in top-level road cycling.
"I do believe that there is still an endemic problem of lower-level doping throughout different levels of our sport," Cookson said Monday.
Still, the UCI chief questioned the claim of one witness in the Cycling Independent Reform Commission (CIRC) report who suggested 90 per cent of top-level riders still dope.
Cookson hopes publishing the report can help turn the page on the doping era and instil confidence that cycling is serious about stamping out cheating.
"We will no longer turn a blind eye to doping, we will no longer assist people in covering up doping," he said.
Cookson's two predecessors, Verbruggen and Pat McQuaid — described respectively in the report as "autocratic" and "weak" leaders — were severely criticized for undermining anti-doping efforts.
"I am surprised and occasionally appalled by some of the things" in the report, said Cookson, citing Armstrong's 1999 Tour win as "an absolutely critical moment" in sending a message the UCI was not serious about stopping doping.
The report confirmed that Armstrong's first Tour title was possible only because the UCI accepted a back-dated prescription for corticosteroids to explain positive tests during the race.
Citing the UCI's "serious breach of its obligations ... to govern the sport correctly," the report also suggested the false medical certificate issued on Armstrong's behalf "should have been reported to the criminal authorities and the relevant medical boards."
The UCI's lack of will to curb Armstrong and other riders in an era "infested" with use of the blood-boosting hormone EPO is made clear in the report.
"Going after the cheaters was perceived as a witch-hunt that would be detrimental to the image of cycling," the three-man investigation panel concluded.
Armstrong was among 174 witnesses from across the sport interviewed by the panel chaired by Dick Marty, a Swiss politician who formerly investigated the CIA's use of secret interrogation prisons in Europe.
"No rider came forward to voluntarily admit an anti-doping rule violation," the report said.
Though Armstrong wants to reduce his lifetime ban imposed by the U.S. Anti-Doping Agency, the report did not include any such recommendation.
It did say that many riders believe doping is still widespread as athletes adapt to evade new tests and detection methods, including the biological passport program pioneered by the UCI.
"A common response to the commission, when asked about teams, was that probably three or four were clean, three or four were doping, and the rest were a 'don't know,'" the report said.
It said the "generally sophisticated" cheating is likely done outside team control by riders meeting with "doping doctors."
Cookson said it was "despicable" that some banned doctors continue to work with riders.
However, clean riders today have a chance of being competitive, helped by the biological passport which monitors their blood changes over time. The micro doses of doping products now used, the report said, boost performance by just "3-5 per cent gains, instead of 10-15 per cent in the EPO era."
The UCI of Verbruggen's era was criticized for "inadequate" policies to combat doping, tolerating use of banned drugs and seeing only excessive use as a health problem.
The report noted that Verbruggen, "with his business experience" as a marketing executive, saw the potential appeal of Armstrong returning as a cancer survivor to cycling after scandal blighted the 1998 Tour.
"UCI saw Lance Armstrong as the perfect choice to lead the sport's renaissance," the report said, adding, "the fact that he was American opened up a new continent for the sport."
Despite the close relationship, the panel said it found no evidence of corruption in Armstrong's payments to the UCI totalling $125,000, allegedly to cover up his suspicious samples for EPO at the 2001 Tour de Suisse and 1999 Tour de France.
The UCI allowed Armstrong's lawyers to draft parts of a supposedly independent report into claims relating to the 1999 samples.
Armstrong said in a statement Sunday he was "deeply sorry for many things I have done."
"I am grateful to CIRC for seeking the truth and allowing me to assist in that search," Armstrong said ahead of seeing the report.