The three had been killed in Hamas's attack on Israel on 7 October and their bodies taken to Gaza.
It says Israel must be forced to stop its operation in Rafah, in a fresh bid to the UN's top court.
Its national broadcaster says it faced hostility simply because "we are Israelis and we were there".
The prison service did not directly address reports 13 prisoners had died since last October.
There are competing claims about the scale of Israel's reported overnight attack targeting Isfahan in Iran.
The unexpected pull-out could mark a new phase in the months-long war.
Israel's Air Haifa to debut in late 2Q24 - minister