However, the Tubbataha reef lies within the Philippine's territory, and is not considered a disputed area.
BBC: China boat 'runs aground' Philippine Unesco coral reef
The 12-man vessel ran aground Tubbataha Reef, a Unesco World Heritage site, late on Monday.
The ship had been 139km (75 nautical miles) south-west of the Philippines' Tubbataha Reef when the coastguard heard of the incident.
BBC: Azamara cruise ship sails for Malaysia after fire repairs
In a statement, the Tubbataha Management Office said the fishermen would face charges for unauthorised entry, damage to the reef, disturbing resources and poaching.
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