"There was no intimidation," Plantations Minister, Mahinda Samarasinghe, told reporters in Colombo.
"No such thing. How can you intimidate them? They don't get intimidated by anyone."
Mr Samarasinghe, who is also the country's human rights envoy to the UN Human Rights Council, said he did not want to comment directly on the report, but added that Colombo was willing to address any shortcomings it raised.
Sri Lankan forces finally crushed Tamil rebels in May 2009 following decades of brutal fighting.
The conflict claimed up to 100,000 lives, according to UN estimates, and both sides are accused of war crimes.
"Events in Sri Lanka mark a grave failure of the UN," the draft report said, adding that the world body should "be able to meet a much higher standard in fulfilling its protection and humanitarian responsibilities".
The report also criticises senior UN staff in Colombo who "did not perceive the prevention of killing of civilians as their responsibility - and agency and department heads at UNHQ were not instructing them otherwise".
It accuses the UN of failing to make public that "a large majority" of civilian deaths were caused by government shelling, a charge Colombo has repeatedly denied.
Former UN manager in Colombo, Gordon Weiss, told the Radio Australia's Asia Pacific the UN didn't do enough to prevent civilian deaths.
"I think that there were people who failed to realise that their primary responsibility was to protect human life," Mr Weiss said.
"The consequence was that we probably didn't do as much as we could've done in that time."
Sri Lanka's High Commissioner to Australia, Admiral Thisara Samarasinghe, said there was no requirement for "independent eyes and ears" at the time, and the UN left the warzone for safety reasons.