"I ask countries which think they can help them to come forward so their fates can be determined more quickly. Hopefully the process will be smooth."
The group were expected to be taken to the Australian-funded Tanjung Pinang immigration detention centre on Bintan island, near Singapore, where their asylum claims will be assessed by the United Nations refugee agency.
Sara Nathan, a spokeswoman for the Global Tamil Forum, an organisation representing Tamils in 16 countries, said the migrants had basically been forced to leave the boat.
"They haven't been told exactly where they're going," she told Al Jazeera.
"I also don't want to go back to Sri Lanka. There's nothing there for me, no house, nothing."
"We had arranged for legal aid to be present during the questioning and during the time that they will be transported but the legal aide was refused access.
"It is of concern that human rights have been violated in Indonesia and we're holding Australia responsible because they put them in that situation knowing Indonesia's record on human rights and Indonesia's treatment of refugees."
The migrants have said they are fleeing persecution in Sri Lanka following the end of the country's civil war in May, and have been refusing to disembark until Australia grants them asylum.
But Australia earlier this month said it would temporarily stop processing asylum claims by Afghans and Sri Lankans in response to a sharp rise in the number of asylum seekers reaching its shores by boat.
Latif, a 21-year-old migrant, said he still wanted to go to Australia but knew it was impossible.
"After six months at the port, I don't wish to be here anymore. Life here is hard ... people keep falling sick," he told the AFP news agency.
"I don't want to stay in Indonesia ... finding work will be hard here. I also don't want to go back to Sri Lanka. There's nothing there for me, no house, nothing."