Vietnamese authorities have charged an Australian human rights activist and two other people over an alleged plot to carry out terrorist activities in the South-East Asian country.

The accusations are heavily disputed by US-based pro-democracy group Viet Tan, which said it believed the men were abducted in what it called "an act of transnational repression".

"We strongly deny these accusations; these are complete fabrications," Viet Tan representative Phong Nguyen said.

Melbourne resident Hiep Tran and his Norwegian-Vietnamese colleague Duc Thuan Nguyen flew to Cambodia from Bangkok on September 15 and have not been heard from in almost two weeks.

Yesterday, Viet Tan said the men never intended to leave Cambodia and accused authorities of forcibly taking the pair to Vietnam.

"In fact, they were planning to leave Phnom Penh the next morning back to Bangkok," Dr Nguyen said.

"There is no logical reason why they would enter Vietnam the night before."

In a statement released this afternoon, Vietnam's Ministry of Public Security said it had caught Mr Tran, Mr Nguyen and one other man trying to illegally enter Vietnam from Cambodia.

The statement also alleged the men confessed to being members of Viet Tan — considered a terrorist organisation by the Vietnamese government — and to trying to illegally enter Vietnam to carry out terrorist activities.

The ministry has now initiated a criminal case against the men but has not said when they will face court proceedings.

Concern about 'fair trial'

Dr Nguyen said he had very little confidence in the country's legal system.

"A lot of people in the past [have] been charged behind closed doors … or being sentenced on predetermined charges.

"The concern here is that these men will not get a fair trial."

Prime Minister Anthony Albanese confirmed today the Australian government was providing consular support to Mr Tran's family.

"That's what Australian governments do for our citizens, and we'll continue to engage directly with the family," he said.

A Department of Foreign Affairs and Trade spokesperson said it was making urgent inquiries with Vietnamese authorities.

Vietnam's Ministry of Public Security said its Security Investigation Agency was continuing to investigate the matter and that it would be handled in accordance with Vietnamese law.

Vietnamese authorities have been contacted for comment, along with the Cambodian and Vietnamese embassies.