Wednesday's violence involved rival groups of monks carrying crowbars and sledgehammers — and is part of a longstanding dispute led by a rebel monastery which opposes efforts by the Orthodox Church to improve relations with the Vatican.
Police posted a guard outside the chapel Thursday to prevent further clashes, while government officials urged calm.
"We condemn these clashes and hope that calm will prevail," Foreign Minister Dora Bakoyannis said.
Three monks who were detained by police after receiving hospital treatment Wednesday were freed on the orders of a public prosecutor.
Monks at the rebel Esphigmenou monastery in northern Greece have turned against other monasteries on the all-male, self-governing peninsula.
They have been declared schismatic and ordered to leave Athos after refusing to recognize the authority of Ecumenical Patriarch Bartholomew I, spiritual leader of the world's Orthodox Christians, who is based in Istanbul, Turkey.
Greece's highest administrative court has also ordered their eviction, but the monks have refused to budge.
The Athos dispute was inflamed three weeks ago, when Pope Benedict XVI visited Turkey and met Bartholomew. The ecumenical patriarch visited Athos in October, and urged the rebel monks to reconsider their position.
Wednesday's clashes occurred between Esphigmenou monks and church-appointed replacements at a chapel and offices of the monastery at Karyes, monastic community's administrative center.
Video footage recorded by cell phone and broadcast on Greek television showed monks using sledgehammers to try and break into the compound where the rebel monks are holed up.
Violence broke out as the rebel monks attacked the intruders with crowbars and fire extinguishers.
Esphigmenou's rebel abbot, Methodius, said his monks had been provoked.
"We were attacked and had to respond," he said. "They should be ashamed to call themselves men of the cloth."
In October, a court in the nearby city of Thessaloniki handed down two-year suspended sentences against nine monks and former monastery members for illegally occupying Esphigmenou's offices. Supplies to the rebel monastery are brought in by supporters using dinghies from the nearby island of Thassos.
Esphigmenou is one of 20 monasteries on Athos, where women are banned.
Five rebel monks remained inside the compound Thursday.
Esphigmenou monastery, one of 20 on Athos, has been the scene of a long-running dispute between Orthodox Church authorities and the rebel monks, who get their supplies from supporters using dinghies from the nearby island of Thassos.