The report suggested the laboratory had "been involved in a widespread cover-up" of positive doping tests and stated that 1,417 samples which the WADA had wanted kept were targeted for "intentional and malicious destruction."
With immediate effect the laboratory is prohibited from carrying out any "WADA-related anti-doping activities including all analyses of urine and blood samples."
It also said that all samples at the center would be moved to another WADA-accredited laboratory.
"WADA has acted swiftly to one of the key recommendations made by the Independent Commission in its report," said WADA president Sir Craig Reedie.
"The Moscow Laboratory is provisionally suspended, and the status of the laboratory's accreditation beyond that will be decided by a Disciplinary Committee which will be formed shortly to review the case."
According to Monday's report, Grigory Rodchenkov, director of the laboratory, ordered that the samples be discarded just days before December's WADA inspection.
He apparently told the WADA team that he decided to "do some cleanup to prepare" for their visit. He later said he misunderstood the instructions he received from WADA about the samples, a claim the report's authors said weren't credible.
The laboratory has 21 days to appeal the decision and is able to take the case to the Court of Arbitration for Sport.
On Tuesday, the International Olympic Committee confirmed it had provisionally suspended Lamine Diack, the former President of IAAF,
from his honorary membership of the organization
The IOC also stated that it has asked the IAAF to take action against "all athletes, coaches and officials who have participated in the Olympic Games and are accused of doping in the report of the Independent Commission."
Meanwhile, Russia scrambled to present a picture of a nation that has zero tolerance for doping.
The Russian Athletic Federation said it "fights severely against anti-doping rules violations by athletes, coaches and other categories of specialists working in athletics."
It added: "All athletes who break anti-doping rules are disqualified regardless of their previous titles and results. The Russian Athletic Federation will continue to fight severely against any attempts of breaking the anti-doping rules and code and will respond in an adequate manner to the particular allegations mentioned in the Commission's report."
Sebastian Coe, the president of the International Association of Athletics Federations, has told Russia it must answer the allegations made in the WADA report by Thursday.
Speaking to reporters Tuesday, Nikita Kamaev, head of the Russian Anti-Doping Agency (RUSADA), said the organization was cleaning up the sport and had been efficient in its work.
"There are problems, but the objective facts, based on statistics, show that the Russian Anti-Doping Agency is quite effective," he said.
Earlier, the Kremlin's spokesman, Dmitry Peskov, described the allegations as "quite groundless."
If they aren't groundless, Russia faces having its track and field athletes banned from next year's Olympic Games in Rio de Janeiro.
Dick Pound, the former WADA president who led the investigation, said such a move would have the backing of the organization.
"For the 2016 Olympics our recommendation is that the Russian Federation is suspended," Pound said. "One of our hopes is that they will volunteer that so they can undertake the remedial work needed.
"If they don't, then it has to play itself out and the outcome may be there are no Russian track and field athletes in Rio. I hope they recognize it is time to change and make those changes.
"If they do the surgery and do the therapy I hope they can get [to Rio]. The idea is not to exclude people from the Olympics."