The vessels entered the 12-nautical-mile band of waters at around 9:30 am local time (0030 GMT), the agency said, the latest in a series of incursions by Chinese government ships in recent months.
The incident Friday comes a week after the first entry by coastguard ships since Beijing combined several agencies under the coastguard flag last month, a development that observers said would involve the arming of more crew.
The island dispute has been cited as a potential flash point that may even lead to armed conflict between the Asian giants.
Chinese media have reported that the unified coastguard agency integrates marine surveillance, the existing coastguard -- which came under the police -- fisheries law enforcement and customs' anti-smuggling maritime police.
Tensions have been building for months around the long-standing ownership dispute over the Senkaku islands, which Beijing claims as the Diaoyus.
In one of the most serious incidents of the row so far, Japan in March said a Chinese battleship locked its weapons-targeting radar on one of its vessels. Beijing denied the charge, accusing Tokyo of hyping the "China threat".
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