Richard McLaren, the investigator who spent much of the last two years deconstructing Russia’s schemes and identifying about 1,000 implicated athletes, indicated that many cases would be hard to prosecute given Russia’s lack of cooperation in providing lab data, and its practice of destroying tainted urine samples that would be plainly incriminating.

Still, sports officials charged with building cases against the 95 athletes in question appear to have never followed up on certain leads. Most notably, none requested interviews with the whistle-blower Dr. Grigory Rodchenkov — Russia’s former antidoping lab chief now living in the United States, whose tell-all account prompted Mr. McLaren’s inquiry report — raising questions about their willingness to discipline a major sports power.

In a letter obtained by The Times, Dr. Rodchenkov’s lawyer wrote to the antidoping regulator on Sunday taking issue with the fact that sports officials had not solicited his client’s testimony and had claimed that Dr. Rodchenkov was unavailable. For more than a year, he has been living in hiding in the United States under protection from the Justice Department, which has investigated Russia’s systematic doping in American sports competitions.

“Dr. Rodchenkov’s alleged unavailability has been cited as one of the reasons for the closure of the investigations of individual athletes,” Jim Walden, the lawyer, wrote. “Dr. Rodchenkov has been willing to cooperate,” he continued, noting that only an Olympic investigator, and no sport-specific officials, had requested an interview.

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Craig Reedie, right, president of the World Anti-Doping Agency, and Olivier Niggli, the agency’s director general. “The system was very well organized,” Mr. Niggli said about Russia’s doping program.

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Fabrice Coffrini/Agence France-Presse — Getty Images

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.”

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Dr. Grigory Rodchenkov, Russia’s former antidoping lab chief, is the whistle-blower who prompted an inquiry into Russia’s doping scheme.

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Emily Berl for The New York Times

The regulator’s exoneration of 95 athletes will most likely be seen as partial vindication by Russia, whose officials have been alternately defiant and conciliatory while consistently disputing that the state played any role in the cheating. Reaction will also most likely be closely watched by the International Olympic Committee, which is continuing its investigations into Russia’s cheating and considering blanket punishments for the nation ahead of the 2018 Games.

While the I.O.C. has opened disciplinary proceedings against dozens of Russian Olympians, no medals from the 2014 Games in Sochi, Russia — where the nation cheated most flagrantly, with Dr. Rodchenkov swapping out steroid-laced urine overnight — have been rescinded.

Nine months ago, the antidoping regulator, which had lobbied to bar Russia from the 2016 Olympics, published 1,166 pieces of evidence of Russia’s schemes, unearthed by Mr. McLaren and drawing on the testimony and computer hard drive of Dr. Rodchenkov.

Although that evidence — including emails, documents and forensic and scientific analysis — effectively proved a doping system, Mr. Niggli said, it did not necessarily translate to prosecuting the athletes Mr. McLaren had identified as having benefited from the program.

Of the 96 cases closed so far, the athlete who has been disciplined, according to the internal report, was prosecuted successfully because officials had recovered an incriminating urine sample from Dr. Rodchenkov’s former laboratory in Moscow. Thousands of other such samples were destroyed, Dr. Rodchenkov said, and the Russian government has made it a crime for investigators to enter a certain storage area in the lab containing other samples.

“The different types of evidence provided with respect to any individual athlete are like strands in a cable,” Mr. McLaren wrote in his report last December. It would be up to the sports authorities, he said, “to determine whether the provided strands of evidence, standing alone or together, build a sufficiently strong cable.”

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