In Beijing, a Chinese foreign ministry spokesman said China had nothing to do with the incident.
"We have learned, that has nothing to do with the Chinese side," he said, declining to give any further comment or explain precisely what was meant by his statement.
Diplomats in Beijing said they were confused by the choice of words, which appeared to be neither a denial nor a confirmation of the reported clash.
The Philippine armed forces statement said Navy chief Vice Admiral Pio Carranza, in a report on the incident, described the intruder as "a PROC [People's Republic of China] vessel with bow number 04420 with red star flag flying on her mast."
A port official said a report he received of the incident mentioned "Chinese military men" on board the ship, while a military officer described it as a naval vessel. Both spoke on condition they not be identified.
Carranza said the exchange occurred in the early hours of Monday when the Philippine gunboat spotted two "suspicious" ships 12 miles off the island of Capones, 75 miles northwest of Manila.
The Philippine boat fired a warning shot for them to stop as they came within 800 yards of each other, Carranza said in his report released by the armed forces press office.
One of the ships fled for the high seas while the other vessel tried to ram the Philippine boat, Carranza's report said.
"A sea gunbattle ensued for about 90 minutes. The enemy watercraft attempted to bump [the Philippine navy boat] but unsuccessfully due to the heavy volume of fire delivered to the target," it added.
The engagement was broken off only when the Philippine ship ran out of fuel as it tried to pursue the Chinese boat and its gun jammed, it said.
Although the armed forces statement quoted the Navy chief as identifying the vessel as Chinese, the Navy spokesman later told a news conference the identity was still being checked.
"We are still verifying it," Commodore Eduardo Maria Santos said. "It was dark, there was lot of firing going on, the adrenalin was high," he said, adding that the crew was now uncertain about the identity of the boats.
The departments of defense and foreign affairs played down the incident. Defense Secretary Renato de Villa, calling it an apparent case of piracy, said the incident occurred when the intruding vessels attempted to intercept a cargo ship.
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