"The world-governing body has imposed this suspension due to an Adverse Analytical Finding of a sample taken at the BWF World Championships in August," BWF said in a statement.
The matter is now before the BWF doping hearing panel which will fix the date and venue for the hearing, it added.
The Badminton Association of Malaysia had on Saturday said one of its top player had failed his second dope test. Traces of the banned drug, dexamethasone, was found in his urine sample. BAM declined to name the player citing BWF regulations.
Lee however had come forward and publicly denied that he cheated in his official Facebook page.
"I just want to thank every one of you who had faith in me through this difficult times. There are so many unanswered questions and I hope to clear my name soon. I never cheated nor will I ever rely on banned substances," he posted on Saturday.
The doping scandal arises from a random test during the World Championships in Copenhagen on August 30 in which he won for second consecutive year.
Lee was a silver medallist in the 2008 Beijing Olympics and 2012 London Olympics.