The External Affairs Ministry said it had received a copy of the report by a three-member expert panel who handed their findings to UN Secretary General Ban Ki-moon Ban on Tuesday.
"The government finds this report fundamentally flawed in many respects," the ministry said in a statement.
"Among other deficiencies, the report is based on patently biased material which is presented without verification," it said.
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The report has yet to be published, and the foreign ministry statement gave no details of the contents it was objecting to.
Soon after Ban appointed the panel in June last year, Sri Lanka called it an "unwanted and unwarranted" interference in its internal affairs and refused to allow the experts to visit the island.
But according to media reports in Colombo, Sri Lankan officials held secret talks in New York in February with the panel, led by the former attorney general of Indonesia, Marzuki Darusman.
According to UN estimates, at least 7,000 civilians died in t