"Torture continues in the system due to weaknesses in law," said Juan E Mendez, the UN Special Rapporteur on Torture and other cruel, inhuman or degrading punishment.
Mendez was on an 8-day visit to Sri Lanka with the UN Rapporteur on Independence of Judiciary Monica Pinto.
Their findings are to be given to the Sri Lankan government and the government's response would be reported at the UN Human Rights Council's next sessions in March 2017, Mendez said.
He said the UN was encouraged by the positive steps taken by the government to uphold human rights values.
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Having visited the detention camps and prisons, Mendez described the conditions as "deplorable" .
"Sri Lanka is at a crucial moment in its history and we hope that our recommendations will continue to setting out a path for the future that will be fully aligned with the international human rights obligations of the country," he said.
The visit of the rapporteurs are in accordance with the UN Human Rights Council resolution of March 2014 when the council prescribed an international investigation on alleged war crimes blamed on both the government troops and the LTTE.
Hundreds of ethnic Tamils have been lodged in jails without trial since 2009, when Sri Lanka's military crushed Liberation Tigers of Tamil Eelam (LTTE) rebels in a three decade-long conflict for control of the island's northern Jaffna peninsula.
According to a UN report, up to 40,000 Tamil civilians may have been killed in the final months of the fighting.