The World Anti-Doping Agency (WADA) has accused Grigory Rodchenkov of being at the heart of a scheme to cover up widespread use of illegal drugs among Russian athletes, including deliberately destroying positive test samples.
WADA suspended Moscow's heavily criticised anti-doping laboratory on Tuesday, the day after releasing its explosive report accusing Russian athletics of corruption akin to that which plagued top-level sport in Communist East Germany in the 1970s and 80s.
"The minister accepted his resignation and one of the specialists at the laboratory was appointed in his place, Maria Dikunets," Natalya Zhelanova said.
The crisis engulfing athletics, long viewed as the flagship of the Olympic Games, comes hot on the heels of a huge corruption scandal at world football's top body FIFA and as cycling is still reeling from the Lance Armstrong doping scandal.
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It has also seen the former president of the athletics governing body IAAF, who on Tuesday resigned as the head of a charitable sporting foundation, charged with corruption.
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IAAF president Sebastian Coe has given the Russian athletics federation (ARAF) "until the end of the week" to respond or risk possible suspension, with the IAAF Council set to meet in Monaco on Friday.
Russia, which came fourth in the 2012 London Olympics medal table, has rejected the accusations as "groundless" and promised a rapid response to avoid suspension from next year's games.