But Israel police flatly denied the allegations, with a spokesman telling AFP they "operate within the bounds of the law."
The letter expresses concern about the growing number of testimonies submitted by Palestinian minors who have been arrested by police in occupied and annexed east Jerusalem, notably in the flashpoint neighbourhood of Silwan.
"We are writing ... to express our deep concerns about the physical and emotional welfare and proper development of children and young people in east Jerusalem in the light of police behaviour during the investigation and arrest of minors in this area," it said.
"Over the last few months, there has been a growing number of testimonies of minors and their families which point to flagrant violations of the rights of detained minors, and of the use of violence during the investigation of children and young people who are suspected of throwing stones in Silwan."
Youngsters have testified how they were dragged out of bed in the dead of the night, cuffed and taken for investigation without being accompanied by their parents -- and sometimes without their family even being informed, it said.
During the investigation, "they suffered threats and humiliation at the hand of the investigators .. which sometimes involved substantial physical violence," it said, noting with concern the arrests of children under the age of 12.
Under Israeli law, the minimum age of criminal responsibility is 12 years, and a child below the age of 14 is not eligible to receive a custodial sentence.
"Despite their young age, they weren't spared difficult and harmful interrogation conditions," it said, citing one case where police had interrogated an eight-year-old for four hours.
Police figures indicate that over the past year, more than 1,200 minors from east Jerusalem have been investigated for throwing stones, the letter said.
Questioned by AFP, Israel police spokesman Micky Rosenfeld denied investigators were flouting the laws governing the rights of minors, although he did admit that police had questioned children under the age of 12.
"We operate within the bounds of the law," he said.
"All the interviews are recorded and we never investigate children under 12 without the presence of a family member. Most of those arrested are older than that."
Testimonies collected by the rights group Defence For Children International (DCI) showed that in the four-week period from October 8 to November 3, 21 minors were arrested in Silwan, two of them under the age of 12.
Meanwhile, a Palestinian man in Silwan on Thursday told AFP that his seven-year-old son Adam had been beaten in the legs and around the face by border police in the street after coming out of school.
A shopkeeper tried to intervene along with other passers-by and the boy had managed to run home, covered with bruises, said his father, Mansur Resheq, who took him to be examined at Sharei Tsedek hospital in west Jerusalem.
The crumbling neighbourhood of Silwan is the focal point of regular clashes between locals and hardline settlers, with police frequently rounding up youngsters on charges of stone-throwing.
The Palestinians see east Jerusalem as the capital of their promised state but Israel considers all of Jerusalem to be its "eternal and indivisible" capital, a status not recognised by the international community.
------------------------------------------------------------------------