The newspaper enlisted two leading anti-doping experts – scientist Robin Parisotto and exercise physiologist Michael Ashenden – who concluded that more than a third of medals, including 55 golds, awarded in endurance events at the Olympics and World Championships had been won by athletes who had recorded suspicious tests. The newspaper claims none of those medals have been taken away by the authorities.

WADA president Craig Reedie said: “WADA is very disturbed by these new allegations that have been raised; which will, once again, shake the foundation of clean athletes worldwide.”

He also announced that given the nature of the allegations, they would be handed over immediately to the organisation’s Independent Commission for further investigation.

Reedie said: “These allegations require swift and close scrutiny to determine whether there have in fact been breaches under the World Anti-Doping Code and, if so, what actions are required to be taken by WADA and/or other bodies.

“As always, WADA is committed to doing what’s necessary to ensure a level playing field for clean athletes of the world.”

It is also alleged that a top UK athlete is among seven Britons with “suspicious” blood scores, while it is also claimed that 10 medals were won at the London 2012 Olympics by athletes who had reportedly recorded dubious test results.

Among the other claims, the Sunday Times says more than 800 athletes – one in seven of those named in the files – have recorded blood-test results described by one of the experts as “highly suggestive of doping or at the very least abnormal”; and that more than a third of the world’s fastest times in endurance events were recorded by athletes whose tests have triggered suspicion.

Parisotto said: “Never have I seen such an alarmingly abnormal set of blood values...So many athletes appear to have doped with impunity, and it is damning that the IAAF appears to have idly sat by and let this happen.”

Ashenden was also critical of the IAAF, saying: “For the IAAF to have harvested millions of dollars from the broadcasting of athletics events around the world...yet only devote a relative pittance of those funds towards anti-doping, when they could see the terrible truth of what lay beneath the surface, is... a shameful betrayal of their primary duty to police their sport and to protect clean athletes.”

The IAAF has so far been unavailable for comment, but it confirmed a statement would be released “once we have studied this, and the Sunday Times article”.

The Sunday Times reported that the IAAF had threatened to take out an injunction preventing the newspaper from publishing details of the files before it dropped its action on Friday.

Sergey Bubka, an IAAF vice-president and candidate for the presidency of the organisation in this month’s election, confirmed an official response to the leak would be following shortly.

The Ukrainian told the BBC that the IAAF had invested more money in catching dopers than any other global sporting body.

“We know that in the 21st century the biggest danger is doping, and there will be zero tolerance,” he said.

“If we need to strengthen our rules and regulations we will do it. We will continue to co-operate with the WADA, and we will continue to co-operate with the IOC.

“It’s zero tolerance and protecting the athletes – this is our firm position.”