The prisoners who are being released in exchange for captured Israeli soldier Gilad Shalit have been officially pardoned.
However President Shimon Peres included a note with the pardon files that said the decision to free them had been made "with an aching heart".
"The voices of the terror victims and the deep grief of their families burns all of our hearts," he said.
"My decision in this matter to exercise my authority in no way pardons or forgives these murderers and criminals. I do not forgive and forget. The sense of loss will never be erased. The heroism of the victims will not be forgotten."
In total, 1027 Palestinian prisoners, including the perpetrators of some of the worst terrorist attacks in Israeli history, are being freed early in return for Sergeant Shalit.