Once Mr. McLaren’s reports described Russia’s doping program, the sanctioning of individual athletes fell into the global sports bureaucracy. The governing bodies for each sport were left to scrutinize their own athletes and mete out punishment when warranted. The World Anti-Doping Agency would then review the decisions made by various sports federations and determine whether they should be approved or challenged. That process has yielded the 95 cases that the antidoping agency has agreed to close.

Some antidoping officials have expressed concern about conflicts of interest among the leaders of individual sports, because they might be inclined to exonerate their own athletes. The head of the global antidoping agency, Craig Reedie, is also a member of the International Olympic Committee, prompting questions about his dual roles of promoting the Olympic brand while also pursuing offenses that could tarnish it.

Each sport’s governing body and the International Olympic Committee have ultimate authority over sanctioning athletes, but the antidoping regulator’s declarations are influential, and the agency has the power to appeal cases.

Mr. Niggli stressed that investigations into other athletes implicated in the doping system were continuing, and that officials needed to pursue the strongest cases first so that they would stand up against the inevitable legal challenges in world sport’s arbitration court. “Leading with a weak case or a poorly prepared case could negatively affect the outcome of all other cases,” the internal report said.

“We have to accept the fact that McLaren’s purpose was to prove a system, not individual violations,” Mr. Niggli said in the telephone interview. “There might have been more evidence out there in Russia for sure, but there was a limit to what he was able to get.”