The RAF has flown 13 Palestinians to Cyprus today in a move to try and end a 39-day stand-off at the Church of the Nativity in Bethlehem.
Elsewhere, several people were slightly injured in a bomb attack in the southern Israeli city of Beersheva.
The 13 Palestinians - described by Israel as "senior terrorists" - were to be held at a hotel on the Mediterranean island until an EU foreign ministers' meeting on Monday in Brussels to determine which countries they would be sent to.
A further 26 militants were sent to the Gaza Strip where they were met by Palestinian officials. Civilians, Palestinian policemen and clergy also emerged from the ancient basilica at first light today.
Peace activists, who had earlier refused to leave the church, also left.
The deal was supposed to lead to an Israeli withdrawal from the biblical town, but it hit a last minute snag over the fate of 10 foreign peace activists who refused to leave the church compound.
The activists sneaked past Israeli troops and into the basilica last week out of solidarity with the Palestinians inside.
Israel has said they will be detained and deported when they emerge. The activists apparently wanted a lawyer present when they left the church.
AP