The prisons' body said on Thursday that the move would limit Barghuthi's ability to direct anti-Israeli attacks from behind bars.
It argues the Palestinian leader has not stopped "his terrorist activity" since arrested by Israeli commandos in the West Bank last year.
He is on trial accused of orchestrating attacks that have killed 26 Israelis.
Barghouthi, 43, has denied the charges against him and accuses Israel of mounting a political show trial. A verdict is pending and he will face life in prison if convicted.
He has been held isolated from other prisoners in an Israeli jail for the past year.
Barghuthi was an organiser of the 1987-92 Palestinian uprising, and was jailed by the Israelis before being deported to Jordan.
He returned during the Oslo peace process - gaining respect among Palestinians for his scepticism about Israel's commitment to land-for-peace deals.
Barguthi was one of the leaders
of the Palestinian intidada
His arrest last year was a coup for Israel, whose forces launched a manhunt for him when they moved into the West Bank.
The leader of Yasir Arafat's Fatah faction in the West Bank, Barghuthi is closely identified with one of its offshoots - the Al Aqsa Martyrs Brigade.