The China Coast Guard's 165-metre "monster ship" entered Manila's 200-nautical mile EEZ on Tuesday, Philippine Coast Guard spokesman Jay Tarriela told a news forum.
The coast guard warned the Chinese vessel it was in the Philippine's EEZ and asked about its intentions, he said.
"It's an intimidation on the part of the China Coast Guard," Tarriela said.
"We're not going to pull out and we're not going to be intimidated."
China claims most of the South China Sea - a conduit for annual ship-borne trade - as its territory. (AP PHOTO)
China's embassy in Manila and the Chinese foreign ministry did not immediately respond to a request for comment.
China's coast guard has no publicly available contact information.
The Chinese ship, which has also deployed a small boat, was anchored 700m from the Philippines vessel, Tarriela said.
In May, the Philippines deployed a coast guard ship to the Sabina shoal to deter small-scale reclamation by China, which denied the claim.
China has carried out extensive land reclamation on some islands in the South China Sea, building air force and other military facilities, causing concern in Washington and around the region.
China claims most of the South China Sea, a key conduit for $A4.4 trillion of annual ship-borne trade, as its territory.
Beijing rejects the 2016 ruling by The Hague-based Permanent Court of Arbitration which said its expansive maritime claims had no legal basis.
Following a high-level dialogue, the Philippines and China agreed on Tuesday on the need to "restore trust" and "rebuild confidence" to better manage maritime disputes.
The Philippines has turned down offers from the US, its treaty ally, to assist operations in the South China Sea, despite a flare-up with China over routing resupply missions to Filipino troops on a contested shoal.
