The leader of a group of 43 Papuan asylum seekers now living in Australia says he has concerns for the long-term safety of two Papuans who have returned to the Indonesian province.

Hana Gobay, from Merauke in Papua, and Yubel Kareni, from Serui, were reunited with family in Papua on Wednesday after contacting Indonesian officials in Melbourne and Canberra in mid-July wanting to return home.

"All refugees want to go home. We became refugees because our home is not safe," Herman Wainggai said in a statement issued through the Australia West Papua Association.

"The Australian government granted asylum to all of the 43 based on this.

"The Australian West Papuan community supports Hana and Yubel in their decision as it is a deeply personal one, but I have concerns for their long-term safety.

"If Hana and Yubel were given assurances and promised money then it is understandable they would think about taking this risk. It is also worth remembering that both have family members living unprotected back in West Papua."

The man and woman were among a group of 43 Papuans who sought political asylum in Australia in 2006, following alleged human rights abuses in Papua.

Australia's decision to grant visas to the group – who arrived on a boat to Cape York in January 2006 – sparked a diplomatic crisis between Jakarta and Canberra.

Their return on Wednesday came just a day after 18 men were arrested after raising the outlawed Morning Star flag in the province, and were found with several home-made weapons.

Indonesia's Foreign Affairs Ministry said the return of the pair might "open the hearts and eyes of those who are still trying to pressure Indonesia" about the controversial Papuan issue.

It also said the pair had been intimidated by other asylum seekers in their quest to return to Papua.

AAP has been unable to contact the pair, but Kareni told a local journalist he wanted to "go back to my family".

Gobay, meanwhile, said she was promised a better life in Australia, but it failed to eventuate.

"I was promised a better life there," she told reporters after alighting in Biak, Papua on Wednesday.

"While I was there I was placed in Christmas Island. I had a chance to work in a wool factory. After we got there (to Australia), each of us had our own activities – we didn't see each other any more."