The announcement of the need to change has come during a joint investigation of the system by The Weekend Australian and the ABC's Four Corners to be broadcast on Monday night.

Last March, in Jerusalem, Barack Obama made a direct appeal to Israelis to consider how Palestinians saw the Israeli Defence Forces as "a foreign army".

"It is not fair that a Palestinian child cannot grow up in a state of their own and lives with the presence of a foreign army that controls the movement of her parents every single day," the US President said.

Israel enforces two legal systems for children in the West Bank: one for Palestinian children and one for the children of Jewish settlers. A Palestinian child accused of a crime is brought before Israel's military court while an Israeli child appears before a civilian court.

A Palestinian child has few of the rights of an Israeli child and is usually arrested by the army in the middle of the night and not permitted to have a lawyer or parent present during interrogation. Sometimes they are placed in adult prisons or in solitary confinement. An Israeli child in the West Bank is almost always arrested by summons and always permitted a lawyer.

Mr Obama's comments followed a UNICEF report that concluded that ill-treatment of Palestinian children in the Israeli military detention system appeared to be "widespread, systematic and institutionalised".

"Children have been threatened with death, physical violence, solitary confinement and sexual assault, against themselves or a family member," the report said.

"Most children confess at the end of the interrogation."

Israel's international spokesman Yigal Palmor told The Weekend Australian that the instances detailed by UNICEF were "intolerable".

He said changes needed to be made in relation to the night-time arrests of the children.

"Basically I think that the question of the arrests is a question that needs to be addressed because once you send soldiers and not policemen to arrest people the whole attitude will be different," Mr Palmor said.

"So we need to train soldiers to behave as policemen and that is something that's not so easy. We are going to do this eventually in these cases."

Former Israeli army commander Yehuda Shaul said that when Israeli soldiers saw settlers attacking Palestinians "our orders are not to intervene".

Mr Shaul has founded Breaking the Silence, a group of 950 current and former Israeli combat soldiers who have given testimonies about human rights abuses they witnessed while serving in the West Bank.

Last month the Israeli government, under pressure from human rights groups, stopped a practice of keeping Palestinian children in outdoor cages at night.

The office of Justice Minister Tzipi Livni confirmed the decision and said it came after Ms Livni became aware that it had been a longstanding practice and had included keeping Palestinian children in the cages during snowstorms.

Sydney lawyer Gerard Horton, who left his practice six years ago to work on the issue, said the night-time arrests could have a damaging effect on families.

"You never know when there's going to be a bang on the door in the middle of the night and soldiers are going to demand that you bring out your children and one of them is taken away," Mr Horton said.

Mr Palmor said Israel was working with UNICEF to help it "re-arrange" the system.

"The natural reaction is that this is an intolerable, these are intolerable cases, and that I would like my authorities to do their utmost to make sure that this will not be repeated and that this will change," he said.