The Sunday Times and German broadcaster ARD/WDR have obtained access to the results of 12,000 blood tests from 5,000 athletes between 2001 and 2012.
According to the newspaper, the evidence - which has been seen by the BBC - reveals the "extraordinary extent of cheating" by athletes at the world's biggest events.
Wada's independent commission will investigate the claims in the ARD/WDR documentary Doping - Top Secret: The Shadowy World of Athletics.
Wada president Sir Craig Reedie said his organisation was "very disturbed by these new allegations... which will, once again, shake the foundation of clean athletes worldwide".
The files belong to world governing body the International Association of Athletics Federations (IAAF), but have been leaked by a whistle-blower.
