Varatharajah's claim after a statement on Friday by Navanethem Pillay, the UN high commissioner for human rights, that she believed 2,800 people had died since January and that a further 150,000 to 180,000 were trapped in the war zone.
But the government disputed the number, saying it came from fighters of the Liberation Tigers of Tamil Eelam (LTTE), whom it accuses of using civilians as human shields.
Mahinda Samarasinghe, human rights minister, said: "If the high commissioner for human rights is concerned about these civilians, then the high commissioner must call on the LTTE to let them go''.
The LTTE responded in a statement that it called on the UN to investigate the military's treatment of civilians.
The statement did not comment on charges made by Pillay that the rebels may have committed war crimes.
The government has rejected calls for a ceasefire in its effort to capture the shrinking LTTE territory that would put an end to Sri Lanka's 25-year civil war.
LTTE fighters are estimated to have been forced to retreat to a 35sq km area in the northeast by the Sri Lankan military.
Government forces are fighting for control of the last LTTE-held town of Puthukkudiyiruppu, about 280km northeast of the capital of Colombo.
Sri Lanka's military has said there is a chance that V Prabhakaran, the LTTE chief, is still in the war zone and has not fled the country.
"There is a possibility Prabhakaran is still there," Brigadier Udaya Nanayakkara, the military spokesman, said. "They are putting up tough resistance and that may be because he is still there."
He said fighting around Puthukkudiyiruppu was continuing, and it was not possible to say how long it would take for the government to capture the town.
The LTTE has been fighting since 1983 for an independent state for the Tamil minority in the Sinhalese dominated majority.
More than 70,000 people have been killed in the fighting.