Colombo's displeasure over a statement by Clinton to the United Nations Security Council was conveyed to US diplomats in the Sri Lankan capital, a foreign ministry official said.
"We have given a note of protest" to the US embassy, the official, who asked not to be identified, said.
In a statement to the Security Council, Clinton last Wednesday made a passing reference to Sri Lanka.
"We've seen rape used as a tactic of war before in Bosnia, Burma and Sri Lanka and elsewhere," Clinton said during a resolution calling for an end to sexual violence in armed conflict.
The remark was contained in a transcript of the statement Clinton made to the UN Security Council that was given to AFP in Colombo by the US embassy.
The state-run Daily News in Colombo reported that Clinton had suggested that Sri Lankan security forces used rape in their battle against Tamil rebels.
The US embassy would not comment on the newspaper's allegations.
Sri Lanka's defence spokesman Keheliya Rambuk