McLaren said the first of three stages of the investigation looked into the refereeing and judging at Rio where controversial decisions in certain bouts made the headlines.
"The seeds of this were sown years before, starting from at least the Olympic Games of the 21st century through the events around 2011 and London 2012," McLaren told a news conference in Lausanne.
"The qualifying competitions along the route to participation in Rio in 2016 were the practice ground for the corruption and manipulation of bouts at Rio.
"At the Olympic qualifiers, the manipulation methodology was fine tuned in anticipation of use in Rio."
McLaren said he could not comment on whether the results of manipulated bouts would be overturned, saying that was not up to him to decide as the lead investigator.
"The information we have will be turned over to the boxing federation," he added.
"If they think there's justification in declaring that the bout was manipulated then, based on the rules at the time, the decision will have to be made."
The report said a comprehensive study suggested at least nine bouts were suspicious while two bouts caused the system to "publicly collapse".
Those include the gold medal heavyweight bout between Russia's Evgeny Tischenko and Kazakhstan's Vassily Levit as well as the bantamweight quarter-final between Ireland's Michael Conlon and Russia's bronze medallist Vladimir Nikitin.
Tishchenko won the gold medal to a chorus of boos from the crowd on a unanimous points decision even though Levit seemed to have landed more punches.
Conlan, who was the reigning world and European Champion, lost on a controversial split decision to Vladimir Nikitin, leading to the Irishman going on an expletive-laden rant on live television after the loss.
At the time, the AIBA had reviewed decisions in over 200 bouts and removed some judges and referees from the Rio Games after boxers said they were robbed.
"Lads I want my medal, get it sorted and I'll DM you my address," Conlan told the AIBA on Twitter after they announced McLaren's findings.
McLaren said the manipulation structure was made possible because key personnel decided the rules did not apply to them.
He added that AIBA's then president Wu Ching-kuo "bears ultimate responsibility for the failures of officiating at Rio and the qualifying events" and that he was supported by his executive director Karim Bouzidi in Rio.
Taiwan's Wu, who had been at the helm of the AIBA for 11 years, was suspended before he stepped down in 2017.
"For example, the executive director seized powers belonging to the permanent commissions. The commissions would let this happen as did the president," McLaren said.
"Once having acquired the power, he (Bouzidi) would oversee the appointment of referees and judges (R&Js) that knew what was going on but would comply with the manipulation or who were incompetent but wanted to continue as an R&J so were willing to comply or turn a blind eye to what was going on."
Frenchman Bouzidi was "reassigned" by the AIBA during the boxing tournament in Rio after numerous controversial decisions.
The report also said the president "avoided discussion of what he apparently knew was inappropriate conduct" in his reports to the International Olympic Committee (IOC).
McLaren added: "Bouts were manipulated for money, perceived benefit of AIBA, or to thank national federations and their Olympic committees, and, on occasion, hosts of competitions for their financial support and political backing.
"Boxing has a problem, it's not about the rules and processes. It's a people problem. For too long people have worked outside the rules."
Umar Kremlev, who took over as AIBA president last year, said they hired McLaren because they had "nothing to hide".