The Israeli army evacuated two Palestinian men needing medical treatment from Bethlehem's Church of the Nativity.
A Palestinian hospital official said a teenager had also escaped from the church but was caught by the army and released for medical treatment. Israeli forces have encircled the church for about two weeks.
Mr Peter Kumri, director of the nearby Beit Jala hospital, said that one man wounded four or five days ago and a second with epilepsy had left on Monday. He said an Israeli army ambulance had taken them away.
Mr Kumri said the wounded man had bullet wounds to the stomach.
An Israeli military source said the army had evacuated two men from the church for health reasons, saying one of them had asthma or epilepsy. It had no immediate comment on the teenager.
Israeli soldiers have surrounded the church, which Christians believe stands on the site of Jesus's birthplace, for about two weeks in a standoff with about 100 Palestinians inside. They include gunmen and dozens of Christian clerics.
Israel has said it has no intention of storming the church, and has proposed a deal under which the gunmen would surrender and be tried in a military court or go into exile "forever".
But the Palestinian governor of Bethlehem, who is among those inside the sanctuary, has rejected the plan.