Dozens of people, including several Israeli police officers, were slightly hurt in the brawl at the shrine, built over the spot where tradition says Jesus was crucified and buried.
Four priests were detained, police spokesman Shmulik Ben-Ruby said.
Custody of the Church of the Holy Sepulcher is shared by several denominations that jealously guard territory and responsibilities under a fragile deal hammered out over the last centuries. Any perceived encroachment on one group's turf can lead to vicious feuds, sometimes lasting hundreds of years.
Monday's fight broke out during a procession of hundreds of Greek Orthodox worshippers commemorating the 4th century pilgrimage by Helena, mother of Emperor Constantine, to Jerusalem. Tradition says that during the trip, Helena found the cross on which Jesus had been crucified.
Church officials, speaking on condition of anonymity, said that at one point, the procession passed a Roman Catholic chapel, and priests from both sides started arguing over whether the door to the chapel should be open or closed.
Club-wielding Israeli riot police broke up the fight, witnesses said. Afterward, the procession continued.
Greek Orthodox priests, dressed in black robes and donning elaborate headdresses, marched out of the church as bells rang loudly. Carrying gold staves and roses, they marched through the church courtyard and down a narrow stone alley as Greek Orthodox Christians clapped and cheered.
In 2003, Israeli police threatened to limit the number of worshippers allowed to attend an Easter ceremony if the denominations did not agree on who would lead the ceremony. Police brokered a last-minute deal and the ceremony passed peacefully.
But a year earlier, the Greek patriarch and Armenian clergyman designated to enter the tomb exchanged blows after a dispute over who would be first to exit the chamber.