The Philippines deployed a second vessel to tiny islands in the South China Sea on Thursday in a bid to assert its sovereignty in a territorial standoff with China.

Authorities said a coast guard boat would join the Philippines' biggest warship in the morning at Scarborough Shoal, where two Chinese surveillance vessels were protecting a group of Chinese fishermen from being arrested.

"It will be backing us up in the area," Navy commander Vice-Admiral Alexander Pama said of the 56-metre-long (184-foot) search and rescue coast guard vessel.

However foreign affairs department Raul Hernandez also emphasised the Philippines was intent on ending the standoff peacefully, and negotiations with Chinese diplomats would continue.

"What is important is that we are talking to them to reach a diplomatic solution. The diplomatic solution should be fair and workable," Hernandez told reporters.

The dispute began on Sunday when Philippine authorities found eight Chinese fishing boats at the shoal, a group of tiny islands and reefs 124 nautical miles west of the country's main island of Luzon.

The Philippines accused the fishermen of being there illegally, asserting the area was Filipino territory because it was within the country's 200-nautical-mile exclusive economic zone, as recognised by international law.

However China claims all of the South China Sea as its own, even waters up to the coasts of other countries, and Chinese authorities insisted the fishermen were allowed to be at the shoal.

Competing claims to the South China Sea have long been regarded as one of Asia's potential flashpoints for military conflict.

The sea holds enormous economic and political significance, as it is believed to sit atop vast oil and gas resources, is home to vast fishing grounds and hosts shipping lanes that are vital for global trade.

Aside from the Philippines and China, Taiwan, Vietnam, Malaysia and Brunei also have competing claims to the waters.

In the latest flare-up in tensions, the Philippines' deployed its navy flagship vessel to Scarborough Shoal immediately after the Chinese fishermen were discovered there, with orders to arrest them.

But the two Chinese surveillance vessels appeared on the scene on Tuesday and blocked the Philippine warship from approaching the fishing boats.

The Chinese embassy in Manila released a statement on Wednesday ordering the Philippine warship out of the disputed waters.

In Beijing, foreign ministry spokesman Liu Weimin accused the Philippines of "harassing" the Chinese fishermen and said a protest had been lodged.

"We urge the Philippine side... not to make new troubles and create conditions for the friendly relations of the two countries," Liu said.

The Philippines and Vietnam complained last year of increasingly aggressive acts by China in staking its claim to the South China Sea.

The Philippines accused Chinese vessels of firing warning shots at Filipino fishermen, as well as harassing an oil exploration vessel and placing markers on islets within Philippine territory.

However this week's standoff is the highest-profile in recent years.