It released the figures to mark Palestinian Prisoner’s Day, which is observed on April 17.
Of the thousands behind bars, 430 are administrative detainees held without charge or trial, including 180 children and 41 women and girls.
There are 550 prisoners suffering from various illnesses, including 11 with cancer, seven with kidney failure, and heart disease. One of the sick prisoners is Foad Shobaki, who is 82.
There are eight prisoners with serious disabilities, said the NGO, adding that 222 prisoners had died in Israeli prisons since 1967.
Prisoner’s Day had become an occasion for paying tribute to the 1 million people jailed since 1967, the Palestine National Council (PNC) said.