Jan Egeland, the UN's humanitarian chief, said that if the government could not protect aid workers, the agency would pull out of Sri Lanka.
"... I say we cannot continue in this area unless people will be held accountable for the execution of 17 of our colleagues," Egeland told reporters in New York.
The UN's top envoy in Sri Lanka, however, indicated the agency was committed to its work on the island.
"Of course we are terribly concerned and we expect the government to do right thing, but right now we are in a major effort to support 200,000 displaced people, and we have a job to do," Miguel Bermeo said on Thursday.
On Wednesday, the Sri Lanka Monitoring Mission (SLMM) accused the army of executing 17 Sri Lankan staff of the Action Contre La Faim aid agency in the northeastern town of Mutur.
The government has denied the allegations and accused the monitoring team of bias toward Tamil Tiger fighters.
The SLMM's EU members are due to cease work on Thursday, after the Tigers ordered them to leave Sri Lanka in response to the EU banning the anti-government group as a terrorist organisation.
Many have already left, reducing the mission by two-thirds to around 20 staff.
In recent months sri Lanka has returned to the brink of full civil war, with both sides launching major military operations.
The Tamil Tigers took up arms against the Sr Lankan government in 1983, claiming that the country's 3.2 million Tamils needed a seperate homeland to end discrimination by the majority Sinhalese population.
At least 65,000 people have been killed in during the conflict.