Bethlehem residents say smoke rose over the ancient basilica. Witnesses said the firing came in two bursts about 15 minutes apart, each lasting for a few minutes.
The Israeli military spokesman said gunmen in the church opened fire and Israeli troops responded.
There was no word of casualties.
A Palestinian policeman contacted by telephone inside the church denied the gunmen had fired, and said the shooting appeared to be part of Israel's psychological campaign to keep the gunmen off balance.
The policeman, known only as Salah, said the Israelis blew up a car near the church compound.
Gunfire and explosions have become routine in recent evenings, as Israel steps up pressure on the gunmen to surrender.
Israel has demanded the surrender of the gunmen, who have been in the church since April 2. Israeli officials say several of the men in the church are responsible for attacks against Israeli civilians. About 50 clergymen also are in the church.
Contacts have been going on in hopes of negotiating a peaceful surrender of the gunmen. However, a formal meeting scheduled for Thursday was called off.
Earlier, about 50 people from the United States and Europe marched toward the church holding bags of bread, sugar and canned food they wanted to take inside. Army soldiers stopped them about 400 yards from the church.
The group sat on the ground, lifted sacks of food onto their heads and sang protest songs.
``They have been held inside the church without food and medicine, and the international community has not yet intervened. So we, as civilians, are attempting to do this,'' said Huweida Arraf, a Palestinian-American from Detroit.
The gunman sought refuge inside the church four days after Israel began its military offensive in the West Bank.