The 31-year-old Jamaica-born boxer returned the positive test three days before his fight against Colombian Oscar Rivas at London's O2 Arena on July 20 but was cleared to fight after attending an independent panel hearing.
Whyte, who beat Rivas on points, served a doping suspension between 2012 and 2014 for a previous offence.
He said before the WBC decision that he was "disappointed with the rubbish" said about him but if his B sample tests positive he faces a potential career-ending ban.
"A sample UKAD (UK Anti-Doping) collected from Mr Dillian Whyte in relation with his bout against Oscar Rivas yielded an adverse finding," the WBC said in a statement.
"In light of that adverse finding, and pending the outcome of the WBC's own investigation and adjudicatory process, the WBC is provisionally suspending the WBC's recognition of Dillian Whyte as WBC interim world heavyweight champion and mandatory challenger of the division."
Whyte would have the opportunity to present his case at an investigative hearing, the WBC said.
Whyte's promoter Eddie Hearn said last week the boxer was "absolutely broken".
Since his comeback, Whyte has fought 18 times, losing only once to compatriot and former world heavyweight champion Anthony Joshua, in 2015.