Russia’s sports minister, Vitaly Mutko, has also denied the allegations while expressing broad contrition. Mr. Mutko has acknowledged “serious mistakes,” but he has stopped short of specifying them or admitting to any state role.

In a statement on Tuesday, the sports ministry said it was “extremely disappointed to hear the speculation that Russian athletes are among those found to have violated antidoping rules at the 2008 Beijing Olympics,” adding, “We have taken numerous steps to eradicate the issue of doping, and understand that the roots of the problem, particularly in athletics, go back to the past.”

Last fall, Russian track and field athletes were banned from global competition after a report published by the World Anti-Doping Agency accused the country of widespread doping. In June, the sport’s governing body will convene to decide whether to lift that ban ahead of the Summer Olympics in Rio de Janeiro, which start on Aug. 5.

The All-Russia Athletics Federation, which oversees the country’s track and field athletes, posted a statement on its website Tuesday, noting that it would not allow athletes with a history of drug violations to compete at the Rio Games. Referring to its “uncompromising fight against doping,” the organization said its “tough decision” had been motivated by a single aim: “to do everything so that clean athletes could take part in the 2016 Olympic Games.”

Russia’s antidoping agency has been decertified by the World Anti-Doping Agency, as has the country’s testing lab, which was run by Dr. Rodchenkov until November, when he was forced to resign, he said. That month, he fled to the United States, and he has been living in Los Angeles since then.

The I.O.C.’s recent re-analysis of the Beijing samples was part of a broader retesting effort ahead of the Rio Games, and an additional 250 samples from the 2012 Summer Games in London — at which Dr. Rodchenkov said top Russian athletes took steroids — are expected to be retested before Rio.