Beijing claims most of the strategic waterway despite a 2016 international tribunal ruling that went against it, and there have been frequent clashes or tense standoffs between Philippine and Chinese vessels.
Brunei, Malaysia, Taiwan and Vietnam also have claims to the waters.
Commodore Jay Tarriela, a Philippine Coast Guard spokesman, said Chinese patrol ships had this year come as close as 60 nautical miles (111 kilometres) west of the main Philippine island of Luzon.
"Their goal is to normalise such deployments, and if these actions go unnoticed and unchallenged, it will enable them to alter the existing status quo," he said in a statement.
He later told reporters Manila had deployed a coast guard ship to the area to challenge the "unlawful" Chinese patrols.
He said the deployment aimed to ensure Chinese patrols "are not normalised, and that this bullying behaviour does not succeed".
Tarriela said the Chinese coast guard deployed three vessels from its Guangdong and Hainan bases to Philippine waters between December 30 and January 11.
The South China Sea confrontations have sparked concern they could draw the United States, Manila's long-time security ally, into armed conflict with China.
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