A senior foreign ministry official said the allegation, made in a US embassy tweet yesterday, would be discussed with visiting Ambassador for Global Criminal Justice Stephen Rapp.
"Our minister (G. L. Peiris) will take it up face-to-face with ambassador Rapp," the official told AFP, asking not to be named.
"It is a baseless allegation. It is uncalled for," he said.
Rapp arrived in Sri Lanka Monday on a five-day visit to meet officials and politicians to discuss Sri Lanka's rights record and attempts at reconciliation five years after the end of war.
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US diplomats in Colombo told AFP the tweet reflected Washington's toughening human rights policy towards Sri Lanka.
"This tweet reflects official government stance," an embassy official said, speaking on condition of anonymity.
Sri Lanka has denied charges that up to 40,000 ethnic Tamil civilians were killed by the army during the push that crushed Tamil rebels fighting for a separate homeland.
The two went to the Uthayan newspaper and met its owner, Eswarapatham Saravanapavan, who is an opposition legislator from the Tamil National Alliance party.
Saravanapavan said his paper had been a target of attack and five of his employees have been killed in recent years, but no suspects have been prosecuted.
The Sri Lankan foreign ministry official said Colombo believed the US charges were aimed at laying the ground for renewed condemnation of Sri Lanka at the March UN Human Rights Council (UNHRC) sessions in Geneva.
Immediately after the US tweets, Sri Lanka's military added it feared a wider campaign by Washington against Colombo.