One of the boys, who was 17 years old when they arrived in March 2013, has served a jail term in an adult prison, was released on parole on Christmas Eve but spent Christmas Day and New Year in immigration detention.

He remains in detention and won't be returned home to his village in Indonesia until next week. The second boy has also been released on parole and put in immigration detention.

Revelations about the plight of the pair, who had little education and came from poor homes that had no electricity and in one case no running water, have attracted criticism from human rights activists, lawyers and politicians who have said they should never have been prosecuted.

The names of the two teenagers have been suppressed but it can be revealed that the Commonwealth Director of Public Prosecutions (CDPP) approved prosecutions against them because they were on a boat that capsized after Australian Customs officers had boarded the boat. Two passengers were killed.

A spokesman for the Attorney-General's department said since late 2010, the CDPP's policy has been that juveniles should not be prosecuted for people smuggling offences unless there are exceptional circumstances.

"The CDPP approved the prosecution of two individuals under s 233B of the Migration Act 1958 for their involvement in a people smuggling venture that resulted in the death of two people. The two individuals were convicted of this offence," he said.

The spokesman said by the time they were sentenced, the teenagers were considered to be adults and were sent to an adult prison.

The boys had been crew on a boat with 93 Afghani and Iranian passengers that capsized near Christmas Island after it was board by two Customs officers, killing two passengers.

They were prosecuted with another man but Judge Felicity Davis from the WA District Court said in her sentencing remarks that the mandatory sentences for people smuggling did not apply to them because they were juveniles.

The judge accepted that they all came from impoverished backgrounds with limited formal education. They were still sentenced to three and half years' jail with a nonparole period of 21 months. It was backdated to include the time they had spent in detention.

However, Greens Senator Sarah Hanson-Young said: "The boys should never have been on trial and sentenced like this.

"The government's policy was to return them to Indonesia immediately and that's what should have happened," said Senator Hanson-Young.

"These were impoverished, vulnerable children who were coerced by people smuggling kingpins. Locking these children in detention, trying them as adults and then dumping them in an adult jail was unnecessary and inappropriate," she said.

"In 2012, I established a Senate inquiry into the government's shocking practice of holding Indonesian minors in adult facilities. The Senate inquiry uncovered dozens of concerning cases and called for significant compensation while a preceding report on this same issue, from the Australian Human Rights Commission, was scathing.

"After those damning inquiries we were told that things would change. It's disappointingly clear that ... mistakes are still being made."

Edwina Lloyd, state Labor candidate for Sydney and a criminal lawyer who has acted for numerous Indonesian minors duped into acting as crew on people smuggling boats, said it is not in Australia's or Indonesia's interest to be jailing impoverished Indonesian children.

"Jailing these children is cruel, inhumane and pointless. Australia has obligations under international human rights law such as the United Nations Convention on the Rights of the Child, which provides that no child should be jailed with adult prisoners," she said.

"These Indonesian children are very vulnerable to manipulation in an adult jail due to their age, lack of education, inability to speak any English and their poor socio-economic circumstances."

A spokeswoman for the Department of Immigration said  the department's only involvement was the initial processing and subsequent detention of the individuals.

She said that non-citizens without a visa are detained in immigration detention and removed from Australia as soon as reasonably practicable.