"The Russian sports ministry, with full responsibility, states there are no government programs to support doping in sport," the ministry said in a statement on Friday, adding that it "will continue to fight against doping with zero tolerance."
Both the Russian Sports Ministry and the Kremlin said they would give a detailed response after studying the World Anti-Doping Agency's (WADA) report.
Dmitry Shlyakhtin, Russia's athletics chief, declined to comment on the WADA report because he had not seen it, according to the Reuters news agency.
Speaking at a press conference in London on Friday, the independent investigator commissioned by World Anti-Doping Agency (WADA), Richard McLaren, said that he and his team had uncovered evidence that Russian authorities in recent years had been involved in a doping cover-up on "an unprecedented scale."
"We are now able to confirm a cover-up that dates back until at least 2011 and continued after the Sochi Olympic Games," he said. "It was a cover-up that evolved from uncontrolled chaos to an institutionalized and disciplined medal-winning conspiracy."
The new findings confirmed and expanded on much of the evidence contained in the Canadian law professor's first report, which was issued in July.
McLaren said that the conspiracy, which involved the Russian Sports Ministry, the national anti-doping agency, and the FSB intelligence service, shielded elite athletes competing in a broad range of summer and winter sports from positive tests.
Responding to McLaren's findings, Vitaly Smirnov, the head of Russia's Independent Public Anti-Doping Commission (IPADC), said Russia has never had an institutionalized system for tampering results of tests for performance-enhancing drugs. The WADA report, he said, describes a "problem not of just one country."
"We see information on a daily basis that athletes from various countries are doping. This is a common evil that must be fought by joining forces," Smirnov was quoted as saying the state news agency TASS.
'Five hundred positive results falsified'
"We have evidence revealing that more than 500 positive results (for performance-enhancing drugs) were reported as negative, including well-known and elite-level athletes, who had their positive results automatically falsified."
McLaren noted that Russia had won 24 gold, 26 silver, and 32 bronze medals at the Summer Olympic Games in London in 2012 and not a single Russian athlete tested positive.
"Yet the Russian team corrupted the London Games on an unprecedented scale, the extent of which will probably never be fully established," he said.
"The desire to win medals superseded their collective moral and ethical compass and Olympic values of fair play."
The second report also revealed evidence that doping samples given by 12 Russian medalists at the Sochi Winter Games had been tampered with. This included athletes who won four gold medals, however they were not identified by name.
He also said that a method of physically swapping urine samples used at Sochi had become a regular practice at the Moscow anti-doping laboratory that dealt with the testing of samples from elite Russian athletes.
He said his conclusions were based on irrefutable forensic evidence, including DNA analysis, which proved that samples had been switched. Other tests that showed that bottles containing samples had been opened when they shouldn't have been.
The first report led WADA to recommend that the International Olympic Committee (IOC) ban all Russian athletes from the Olympic Games in Rio de Janeiro. However, the IOC declined to issue a blanket ban, choosing instead to leave it up to the governing bodies of the individual sports to decide whether Russian athletes would be allowed to compete.
shs/se (Reuters, dpa)