The laboratory, suspended for a maximum of four months, has 21 days to appeal the decision to the Court of Arbitration for Sport (CAS).
"The suspension, which takes effect immediately, prohibits the laboratory from carrying out any WADA-related anti-doping activities including all analyses of urine and blood samples," WADA said in a statement.
WADA said the laboratory could apply for reinstatement before the four months was up if it took remedial steps and tackled "non-conformities", without providing details.
China's national anti-doping agency said the laboratory had submitted "two false negative results" during blind tests conducted by WADA in 2015.
"The laboratory will resume testing work after its changes have been reviewed by WADA," the agency said in a statement on its website (chinada.cn).
State news agency Xinhua later quoted the laboratory as saying that the false negative results were caused by "technical errors" because it had yet to update testing methods to meet WADA's latest requirements.
The laboratory was also negligent in its analysis, it said.
"At present, the laboratory is undergoing a complete review and improvement of its detection methods, in order to meet WADA's latest requirements," Xinhua quoted the lab as saying.
NEWSPAPER REPORT
China's anti-doping programme has been under scrutiny in recent weeks following a British newspaper report that alleged Chinese swimming had covered up positive drugs tests ahead of Olympic trials for the Rio de Janeiro Games to avoid a "storm".
The Times report prompted WADA to investigate the allegations.
China's anti-doping agency denied there had been a cover-up and said they needed time to test secondary 'B' samples and conduct hearings before releasing further information.
The Chinese Swimming Association subsequently announced it had issued a "warning penalty" to swimmers Wang Lizhuo and An Jiabao after they tested positive for the banned substance clenbuterol.
A third swimmer Zhao Ying, who also tested positive for clenbuterol in an out-of-competition test, was named but had not yet been punished, the association said last month.
The country's anti-doping agency courted controversy in 2014 after keeping a three-month drugs ban handed to Olympic 1,500 metres freestyle champion Sun Yang under wraps for six months.
China (five golds) finished second to the United States (16) in the swimming medal table at the 2012 London Olympic Games and are tipped to be a force at the Rio Games.
WADA also revoked the accreditation of a Moscow anti-doping laboratory in Russia for failing to meet standards last Friday.
The lab had been non-operational since WADA suspended it in November after an independent commission's report identified systematic failures within Russia's anti-doping programme.
Russia is currently suspended from international track and field in the wake of the report exposing widespread cheating and corruption and its athletes could miss the Rio Olympics.
(Writing by Ken Ferris and Ian Ransom; Editing by John O'Brien)
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