Barak saidhe "fully backs" Gabi Ashkenazi on the issue.
Ashkenazi's letter, published Monday, said the release was ethically problematic as long as IDF soldier Gilad Shalit was still being held captive in Gaza.
However, the chief of staff and senior officials in the security establishment approved the release of Palestinian prisoners anyway, after deciding such a move would not pose a threat to Israel’s security.
In his letter, Ashkenazi did not oppose the release of prisoners, or attempt to prevent it, but merely expressed his feelings about the process.
Twenty-nine Palestinian security prisoners, whose release from Israeli prison was delayed Monday, were freed from Ktziot Prison Tuesday morning.
President Shimon Peres, who signed the clemency orders for the prisoners, refused initially to sign the release orders for the Gazan security prisoners.
Aides to the president refused to comment on rumors that Ashkenazi’s letter was the reason for the delay.
Fifty-six other prisoners from the West Bank were released Monday.