Norza Zakaria, deputy president of the Badminton Association of Malaysia (BAM), told a press conference that the player's B-sample tested positive for banned anti-inflammatory dexamethasone.
Lee reportedly flew to Norway to witness the second test this week following a positive result in an initial test.
But Norza said the player could not be named pending due process, including a hearing by the Badminton World Federation.
The date for that hearing has not been set, he said.
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Reports of a failed drugs test by the long-time number one, one of badminton's top stars with a reputation for humility and diligence, have shocked followers of what is one of Asia's most popular sports.
Badminton is unused to doping scandals with previous controversies mainly stemming up from judging inconsistencies and attempts to throw matches.
"I would like to inform you that we believe that this player is a very hard-working player and an exceptional individual," Norza said Saturday.
Norza said officials were still probing how the substance -- which he said was not a performance enhancing but a rehabilitative drug -- could get into the shuttler's system.