"I deny having signed any such letter. It is neither in my character nor in the principles of my party -- the CPM -- to petition any sovereign country on matters that fall strictly within the sovereign domain of that country," he said in a statement.
"It is this very principle that leads us to strongly oppose and denounce any external interference into India's internal affairs undermining its sovereignty," Yechury said.
His statement came amid reports that he was among 65 Members of Parliament who had written letters to President Barack Obama, urging the US Administration to maintain the current policy of denying visa to Modi.
Observing that "much of this controversy is taking place in cyberspace," he said, "The one circulating in cyberspace, now many months after it was allegedly signed, is typed on the letterhead of a Member of Parliament which carries the insignia of our national symbol, the Ashok Chakra.
"The heading under which some signatures are appended says, 'Names and Signatures of Indian MPs'. Strange. Which other country's MPs would sign on the letterhead of the Indian Parliament? This, itself, suggests some efforts at cut and paste," Yechury said.
The CPM leader had on Tuesday made a similar statement when he was contacted for his comments on the matter.
He had told PTI that "I would be the last person to write to the US Administration and to do something like this. We don't want anyone to interfere in the internal affairs of the country. These are issues which will have to be settled in India politically."
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