"Every year 700 children are arrested, detained and face ill-treatment in the Israeli military justice system. During 2014, an average of 197 children were held in military detention every month," the group said.
The report published on Tuesday came a week after an Israeli military court sentenced a 14-year-old Palestinian girl to two months in jail and fined her over $1,500 for allegedly throwing stones and carrying a knife.
CRIN estimated that the majority of arrests are on charges of so-called security violations. The vast majority of minors detained by Israeli security forces in the seized Palestinian territories of West Bank are older than 16, the watchdog added.
The rights group argued that Israeli security forces discriminated against Palestinian minors because of their nationality.
Israeli troops took over the West Bank after a six-day war in June 1967. Some 80 percent of the territory's population is comprised of Palestinian Arabs, the remainder are Israeli settlers who moved into the area over 47 years of occupation.
According to CRIN, people of Arab descent are subject to both Palestinian legislation and Israeli military laws. This leads to much harsher detainment conditions for seized Palestinian minors, including the routine of solitary confinements and interrogation in the absence of adults, in an infringement on UN conventions regarding the rights of children.