West Papuan independence activists and their supporters in Australia have accused Jakarta of using students to spy on them.

Lateline has been told postgraduate students are providing information to Indonesian intelligence about Australian citizens and has obtained photos that are claimed to be of some of the student spies.

The pictures were taken in June when the self-proclaimed Federal Republic of West Papua (FRWP) opened an office in Melbourne, as the West Papuan community and its supporters celebrated what they saw as a landmark in their long-running campaign for independence from Indonesia.

The celebrations were interrupted when three men, who had never been seen at any independence movement events, were seen recording the proceedings on smartphones.

The "foreign minister" of the FRWP, Jacob Rumbiak, confronted one of the men and was told they were there to gather information for the Indonesian government.

"He's explained that he's studying a PHD at a Melbourne university and that also he works in the (Indonesian) department of foreign affairs. So he works in the government of Indonesia," Mr Rumbiak said.

He said the man explained he would be reporting back to Indonesian authorities.

"Another two also came and they took photos of this office. I think that the photos they took were sent to the Indonesian government by intelligence," Mr Rumbiak said.

Jacob Rumbiak said he confronted men he accused of spying on the celebration.

The ABC has indentified and contacted one of the three Indonesian men who attended the opening of the office and asked for his version of events, but he has not responded.

The man is a post-graduate economics student at a university in Melbourne, and his Facebook page lists his employer as the Indonesian finance ministry.

The Indonesian embassy rejects the claims.

"The Indonesian Government does not assign its students studying in Australia, or anywhere, to collect/gather information from any sources," the embassy said in a statement.

"The possibility of Indonesian students' presence at open-to-public events, including Papua-related ones, might relate to their studies or personal interests."

Melbourne-based independence movement hacked and harassed

The West Papuan independence movement is strongest in Melbourne.

They said aside from low-level harassment, their office website has also been hacked twice. They claim they were able to trace the IP addresses of the computers threatening the website to addresses in Jakarta and Melbourne.

"We are faced with Jakarta. I do believe that's them and we also have a monitoring system so we can know from which county and the address," Mr Rumbiak said.

The Indonesian Embassy in Canberra denied the attack originated from its foreign affairs offices.

"We can confirm that the Indonesian Ministry of Foreign Affairs is not involved in that website hacking incident, as the ministry does not have a policy nor intentions to hack other institutions."

Anglican minister Peter Woods, who has long campaigned for an independent West Papua, said incidents like this are becoming more frequent and blatant.

"It seems to be very blatant. It's well known amongst the activist community that this does go on," he said.

"It seems overt and not very subtle."

Australian security services aware of student spies: academic

At a talk Reverend Woods gave in Melbourne last month describing his most recent trip to West Papua, he asked two men of Javanese and Timorese origin to leave before he started as he believed they were there as informants.

Activists wave flags during a celebration for the opening of a Melbourne Federal Republic of West Papua office.

"I was about to speak and we noticed that there were two non-Papuans there and we spoke to them and realised that they were agents doing surveillance. We asked them not to be there," he said.

Lateline has spoken to several academics who all believe it is not uncommon for Indonesian post-graduate students to also provide intelligence to their country's consulates or embassy.

"A number of students have been found to have been reporting to the consulate in Melbourne over the years," said Damien Kingsbury from Deakin University.

"As academics, we deal with these students and we know what they are doing. They often tell us what they're doing so we do know they report to their consulates. They do act as spies."

Mr Kingsbury was an adviser to the Free Aceh and Timorese independence movements, and said Australian agencies are aware of this sort of intelligence gathering, but overlooked it due to it proving a comparatively low threat to Australia's interests or security.

"The Australian security services see this as low level activity. They don't see this as more formal espionage and a lot of the information that's being picked up is open access anyway," he said.

However, he said he does believe boundaries are being crossed.

"They also report on private conversations, so that is of more concern," he said.

In the coming weeks a crucial meeting to garner support from Pacific nations for the West Papuan movement will be held in Vanuatu.

Indonesia's president-elect Joko Widodo has indicated he is not opposed to dialogue with the independence movement about their desire for more autonomy, but Jakarta remains firm that independence is off the table.

Watch the full report on Lateline at 10.30pm on ABC TV.