Reacting to a report that she had sought Thapa's removal from the TOP scheme, Mary Kom issued a statement to deny having made any such remark at the meeting which took place on Friday.
"The article states that I have termed Shiva Thapa's career as over and he would do nothing at the 2020 Tokyo Olympics. This is completely fabricated and it borders on being defamatory," Mary Kom said in her statement.
"Playing with the reputation of a hardworking boxer using falsehood is not acceptable to me."
The 23-year-old Thapa is currently preparing for the World Championships, where he won a bronze medal in 2015, at a training trip in France. He recently won a silver medal at the Asian Championships in Tashkent.
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Mary Kom also denied saying that former Commonwealth Games Manoj Kumar was past his prime. The 30-year-old Manoj has also qualified for the World Championships to held from September 25 in Hamburg.
"...This kind of stories without proper verification of facts is tantamount to playing with my reputation," she added.
Mary Kom is one of the two national observers appointed by the Sports Ministry for boxing, other being former CWG gold medallist Akhil Kumar.