Indonesian prosecutors have demanded jail terms of up to 12 months for three soldiers accused of disobedience after they filmed themselves torturing Papuan civilians.

In footage posted on YouTube last year, the soldiers apply a burning stick to the genitals of an unarmed man and threaten another with a knife as they interrogate them about the location of a weapons cache.

The United States has said it is "monitoring" the court martial after human rights activists slammed Barack Obama's decision last year to re-open military links with Indonesia's notorious special forces.

The soldiers each read the same confession to their separate courts martial in the Papua provincial capital Jayapura. "I committed the act. I regret it and promise not to do it again," each said.

The Indonesian military has described their actions as "unprofessional" but has not charged them with more serious offences such as assault or kidnapping. Indonesia has no law against torture. The charge of disobedience carries a maximum penalty of 2 1/2 years in jail.

"Their superiors had never ordered them to abuse the public," each of the three prosecutors said.

Prosecutor Major Soemantri recommended Second Sergeant Irwan Rizkiyanto be jailed for 12 months for disobeying an order, slapping victim Tunaliwor Kiwo and "stepping on his head with flip-flops".

First Private Yakson Agu was accused of suffocating Kiwo with a plastic bag for "10 seconds" and burning his "genital area", and should be jailed for 10 months, prosecutor Lieutenant Colonel Edi Imran said.

In the third case, Imran said First Private Tamrin Mahan Giri deserved nine months' jail for "holding a knife at the neck, lips and nose of victim Telangga Gire".

The minor charges and the authorities' alleged reluctance to investigate the torture allegations cast doubt on the Indonesian government's pledges to rein in military abuses in return for renewed US military exchanges.

The victims have refused to testify at the court martial, saying they fear for their lives and have not been given adequate security guarantees.

In a videoed statement, Kiwo has told Papuan elders he thought he was going to die during two days of torture in which he was repeatedly beaten, suffocated, burned with cigarettes, cut with a razor and tormented with pain.