A human rights organisation has released a report saying children seeking refuge in Indonesia are being locked up, abused and neglected in detention centres.

Human Rights Watch says Australian Prime Minister Julia Gillard should speak with President Susilo Bambang Yudhoyono about improving the treatment of asylum-seeking children so they're less likely to make the dangerous boat journey to Australia.

"The Australian Government has a strong interest in improving conditions in Indonesia," Alice Farmer, a children's rights researcher at Human Rights Watch, said.

"It's just not reasonable to think that the current measures alone will stop people taking these boats.

Space to play or pause, M to mute, left and right arrows to seek, up and down arrows for volume. Listen Duration: 5 minutes 10 seconds 5 m Alice Farmer speaks to Asia Pacific Download 2.4 MB

"You have to look to the north and see if it's possible to improve the conditions here (Indonesia) so that people are less willing to take these risks."

Researchers at the organisation spoke to about 100 migrants between the ages of 5 and 66 who "described guards kicking, punching, and slapping them or other detainees."

The migrants interviewed for the report include those who were children when they entered Indonesia.

"Guards tied up or gagged detainees, beat them with sticks, burned them with cigarettes, and administered electric shocks," the report said.

Alice Farmer, a children's rights researcher at Human Rights Watch, has told Radio Australia's Asia Pacific about a boy from Afghanistan whose first attempt to get to Australia ended with the boat sinking.

"He told me that there is no life for him in Indonesia, there is no future at all," Ms Farmer said.

"I do think if conditions were even a little better in Indonesia, a boy like Arif wouldn't be willing to make that journey (to Australia) again."

Human Rights Watch says more than 1,000 unaccompanied children arrived in Indonesia in 2012.

These unaccompanied children, travelling without parents or other adults, fall into a legal void.

According to Ms Farmer, with no government agency responsible for their guardianship, no one responds to the children's needs.

"They have absolutely no help from the Indonesian government," she said.

"Without any recognition from the government, sometimes they languish in detention longer than the adults because they can't be released at all.

Human Rights Watch says the detention centres in Indonesia fall short of international standards.

"Indonesia doesn't have any asylum law and hasn't signed the 1951 Refugee Convention," Ms Farmer said.

"UNHCR, the UN refugee agency, is present in Jakarta and it does try to offer some help but it doesn't have the capacity to give the children the legal status in Indonesia."

Almost 2,000 asylum-seeking and refugee children were in Indonesia as of March this year, a number that has steadily increased over the last five years.

Ms Gillard is due to visit Jakarta next week to meet with President Susilo Bambang Yudhoyono for their annual talks.