Malaysian authorities sent the three men back to Sri Lanka on Monday after arresting them on May 15 on suspicion of involvement with the Tamil Tigers separatist group.
The United Nations High Commissioner for Refugees (UNHCR) said it regretted the deportation without being given access to the men, who were registered with the agency.
"UNHCR is ... deeply concerned that these deportations took place without the office being given an adequate opportunity to assess these security issues and the refugees' entitlement to ongoing refugee protection," UNHCR Malaysia spokeswoman Yante Ismail said.
New York-based Human Rights Watch also urged Sri Lankan authorities to ensure the safety of the three, who are now reportedly in custody there, saying they were at "grave risk" and could face torture.
"Malaysia's forced return of these refugees to Sri Lanka is no free pass for torture and mistreatment," Phil Robertson, the rights group's deputy Asia director, said in a statement.
"Malaysia seemed more interested in burnishing its ties with Sri Lanka than honouring its obligation to protect refugees from possible persecution and torture."
More than 140,000 refugees and asylum-seekers stay in Malaysia with at least 4,000 from Sri Lanka, according to UNHCR.
Sri Lanka's 37-year bloody separatist war effectively ended five years ago when troops killed the leader of the Tamil Tiger rebels in a brutal assault, but sympathisers remain.
The Tamil Tigers, who were notorious for their suicide bombings, had fought for a separate homeland for Sri Lankan Tamils who account for just over 10 percent of the island's population.