The laboratory had been suspended on November 10 as recommended in the WADA independent commission report that laid bare evidence of state-sponsored doping and corruption in sport in the country.
The report found that laboratory director Grigori Rodchenkov had ordered close to 1,500 samples to be destroyed, prompting the disgraced director's resignation.
A statement today said the lab's accreditation was revoked "due to non-compliance with the International Standard for Laboratories and the related Technical Documents."
"The revocation, which has been accepted by the Laboratory, will enter into force immediately and means that the Laboratory will continue to be prevented from carrying out the testing of doping control samples on behalf of WADA or any testing authority," WADA said.
"The decision was taken by WADA's Executive Committee following a thorough review of the status of the Laboratory by an independent WADA appointed Disciplinary Panel."
Russian sports minister Vitaly Mutko voiced optimism that the move was a first step toward re-accreditation of the lab.
"It's a wise decision and I hope the process of (Moscow's) laboratory's re-accreditation will now start promptly.
"When the lab's work is suspended you just wait for another six months, while its re-accreditation is a kind of a guarantee. What would you choose?" Mutko said.
But the Russian Athletics Federation remains under scrutiny, with new head Dmitry Shlyakhtin working to overturn a ban by the International Association of Athletics Federations (IAAF) over allegations of systematic doping that could see Russian track and field stars sidelined from the Rio de Janeiro Games in August.