Wanniarachchi, 30, Sri Lanka's only gold winner at the Games, tested positive for the performance-enhancing steroid nandrolone, according to a report sent to Colombo over the weekend by organisers of the New Delhi Games.
"We have taken his medal into our custody pending the completion of inquiries," National Olympic Committee chairman Hemasiri Fernando told reporters in the capital.
"He has two weeks to make a written submission.
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The boxer faces a two-year ban and will be stripped of his medal if his "B" test also proves positive.
Fernando said that Wanniarachchi may have unknowingly taken the banned steroid when he consulted a physician several months ago.
"If that is indeed the case, we will plead for a lenient punishment," Fernando said.
A sports ministry official said their probe will extend to the physician who treated Wanniarachchi. Police had already interviewed the physician, a police source said, adding that investigations were under way.
Wanniarachchi beat W