China has been rapidly expanding its occupied reefs in the Spratly archipelago, alarming other claimants and drawing sharp criticism from the United States, Japan and Europe.
The fishing boat was reportedly near a reclaimed reef when the shot was fired.
“If indeed this happened, it is a cause of grave concern,” Philippine defence minister Voltaire Gazmin told journalists in a text message from Tokyo, where he has been accompanying president Benigno Aquino on a four-day state visit.
In Tokyo, Mr Aquino signed a Visiting Forces Agreement that will allow Japanese military aircraft and naval vessels to use Philippine bases to refuel and resupply.
The move will extend Tokyo’s range of operations into the South China Sea.
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China claims most of the South China Sea, through which $5 trillion in ship-borne trade passes every year.
The Philippines, Brunei, Malaysia, Taiwan and Vietnam also have overlapping claims.
All but Brunei have fortified bases in the Spratly Islands, which are roughly 1,300 kilometres from the Chinese mainland but much closer to the South-East Asian claimants.
Japanese prime minster Shinzo Abe voiced his concerns about changes to the current arrangements.
“We once again confirmed that we share serious concerns about China’s large-scale land reclamation and that we oppose any attempt to unilaterally change the status quo,” he said.