Most of those detained were aged between 14 and 17, but some were as young as 12, according to a report by the Palestinian section of Defence for Children International, an organisation set up to protect children's rights. Sentences of a year for stone-throwing were routinely passed on the recommendation of prosecutors, the report claims.
The report adds that many children were arrested at night, when security forces entered their homes following demonstrations.
George Abu Al Zulof, DCI's executive director, said children had been placed in isolation cells or had been asked to stand for hours on end. "In some cases children have been put in cells with loud music playing so they cannot sleep. This is psychological and physical torture," he said.
Under the United Nations Charter on the Rights of the Child, which Israel signed in 1991, the arrest or imprisonment of a child under 18 should be used "only as a measure of last resort and for the shortest appropriate period of time".
Mr Abu Al Zulof said the treatment of the children breached both the charter and the UN Convention Against Torture.
This week teachers in Palestinian areas told British MPs that they were struggling to maintain a normal curriculum because pupil numbers had been affected by the arrests as well as by injuries and some violent deaths. On the days of big Palestinian demonstrations attendance at schools is negligible and Israeli shelling prevents many pupils and teachers leaving home. Israeli security check-points often stopped them reachin school if they risked the streets, they said.
Children aged between 12 and 14 were arrested and tried under military order number 132, which was first used in the "intifada"or uprising of the late 1980s but which had fallen into disuse until trouble flared again recently, Mr Abu said. Older teenagers were tried in civil rather than military courts.
This week a delegation of MPs led by the aid charity War on Want visited Hussan school, near Bethlehem, which was missing 21 children, all of whom are in prison. Another Hussan pupil, a 14-year-old, was killed by an Israeli settler's car in November. The vehicle drove over a traffic island before hitting him on the pavement and then reversing over his body several times.
Pictures of child "martyrs" are plastered on almost every wall in the school, and in one class at nearby Beit Jala a home-made poster, possibly the result of an English lesson, read: "Big shame, Israeli soldiers enjoy killing Palestinians."
The manager of Hussan school, Mohammad Omar Shakarneh, has filled a large bag with CS grenades, tear-gas cannisters, plastic and rubber-coated metal bullets collected from his playground.
"The current situation has affected the school very negatively. Psychologically, financially and just in general," he said.
A spokesman for the Israeli foreign office said he was not aware of the arrests but would make inquiries. "Imprisonment is subject to judicial review, and Palestinians have access to the Supreme Court," he said.
The spokesman added that many of the demonstrations had been extremely violent and adult Palestinians with guns had sometimes been stationed behind stone-throwing children.