Refugee advocates say a Sri Lankan man who died in Sydney's Villawood Immigration Detention Centre overnight poisoned himself.

The Immigration Department says the detainee died after being found in a "distressed state" in his room shortly after midnight.

Ian Rintoul from the Refugee Action Coalition says the man, who was in his early 30s, was a declared refugee waiting for his security clearance to be approved.

"A Tamil refugee [who] has been in detention for over two years has committed suicide. He took poison last night and has died," Mr Rintoul said.

Police are investigating the cause of the death, which is expected to be referred to the Coroner.

Mr Rintoul says the man was granted refugee status a year ago but had been waiting since for a security clearance.

"He could have been out of detention. There is something like 1,500 people inside the detention regime who have been recognised as refugees and have been waiting for security clearance," Mr Rintoul said.

"ASIO has said they don't require people to be in detention while they make these security assessments."

Mr Rintoul says the man was generous and outgoing.

"He was always willing to do anything to help other people," he said.