Bethlehem standoff ends

The first of the 13 militants walks through a metal detector outside the church on Friday.

BETHLEHEM, West Bank (CNN) -- As morning broke Friday in Bethlehem, Palestinians holed up inside the Church of the Nativity began leaving after an agreement was ironed out to end the five-week standoff at one of Christianity's holiest sites.

Escorted by church officials in the presence of the Israeli military, the first of the men -- a group of 13 Palestinian militants wanted by Israel -- emerged from the church compound and passed through a metal detector before departing in a bus. One of the men, who was injured, was taken from the compound in a stretcher and left in a separate vehicle.

The 13 militants will be resettled in the European Union as part of the agreement reached Thursday. Under the agreement, the 13 are to be distributed among countries including Italy, Spain, Austria, Greece, Ireland and Luxembourg, CNN's Chris Burns reports.

Many waved to family members and other Palestinian onlookers, perched on a nearby rooftop. The crowd, also guarded by Israeli forces, waved back and wailed as some of the men emerged.

After they left the compound escorted by U.S. Embassy vehicles, the 13 militants headed to an Israeli military base for identification. From there, they will board a British military plane at Ben Gurion Airport and head to a British air base in Cyprus.

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The government of Cyprus released a statement Thursday confirming it had agreed to allow the militants to transit through Cyprus before moving on to the EU.

Where the 13 militants -- called "senior terrorists" by Israel -- would go into exile has been a key sticking point in efforts to end the impasse at the church, which Christian tradition holds is built on the site where Jesus was born. Earlier in the week, efforts to end the standoff stalled when Italy refused a request to accept all 13 of the militants.

Palestinian legislator Hanan Ashrawi said Israel has presented no evidence that the men were terrorists, saying their deportation was a violation of international law.

"This is entirely unacceptable," she said.

Twenty-six other Palestinians, who could face trial on terrorism charges in Palestinian courts, began to emerge after the first group departed. They will be questioned by Israeli forces, then driven to Gaza, the IDF said.

About 85 other Palestinians not wanted by Israel will leave the compound last. They will be taken to Gushatzion police station, where they will be questioned and released, according to the IDF.

Israel and Palestinian negotiators tried Thursday morning to work out an interim arrangement that would leave the 13 in the church until there was a place for them to go. But sources inside the church said that plan hit a snag when the Palestinians demanded that EU envoy Alistair Crooke be allowed to stay with them inside the church to assure their safety.

Another remaining snag was said to be whether the Palestinians would surrender the weapons they had with them to the Israelis. On Wednesday, a proposal was made for the Palestinians to leave the guns in the church, where they would later be reclaimed by the Palestinian Authority. But Thursday, Palestinian sources said what will happen to the weapons inside the church remained an outstanding issue.

On April 2, Israeli tanks and troops entered Bethlehem as part of "Operation Defensive Shield," a military campaign Israel said was intended to dismantle the "terrorist infrastructure in the Palestinian territories."

As the Israeli troops moved in, Palestinian gunmen went into the Church of the Nativity. The Israelis alleged the Palestinians had taken the nuns and priests inside as hostages. That was disputed by the priests, who said they had stayed to provide refuge for the fighters and to protect the church.

-- CNN Correspondents Walter Rodgers and Wolf Blitzer contributed to this report.