Two Japanese destroyers and one of the Philippines' newest warships began historic naval exercises in the flashpoint South China Sea on Tuesday, showcasing a deepening alliance aimed at countering a rising China.

The day-long war games, the first bilateral naval exercises between the former World War II enemies, took place less than 300 kilometres (186 miles) from a Philippine-claimed shoal now under Chinese control.

Philippine authorities insisted the exercises were merely focused on building military capabilities, but security analysts said they were clearly a signal to China over bitter maritime territorial disputes.

"First they demonstrate that China's Pacific neighbours are beginning to balance against China," professor Michael Tkacik, a foreign policy expert at the Texas-based Stephen F. Austin State University, told AFP.

"Japan, the Philippines, Vietnam, and assorted other states are threatened by China's behaviour, even as far away as India. Thus, the Philippines and Japan are jointly making an important statement about how seriously they view China's actions."

China has caused deep concern regionally in recent years as it has become more aggressive in staking its claims to the South China Sea and Japanese-claimed islands in the East China Sea.

China insists it has sovereign rights to nearly all of the South China Sea.

However the Philippines, Vietnam, Malaysia and Brunei have competing claims to parts of the sea, which is vital to the global shipping industry and is believed to contain huge deposits of fossil fuels.

- Chinese control -

In 2012, China took control of Scarborough Shoal, a rich fishing ground within the Philippines' exclusive economic zone and more than 650 kilometres from the nearest major Chinese landmass.

Chinese coastguard vessels have since guarded the shoal and denied Filipino fishermen access, triggering a series of protests from the Philippines that have been brushed aside in Beijing.

Although the Philippine Navy declined to say exactly where Tuesday's exercises took place, it said the vessels would sail into the South China Sea from a former US naval base in Subic Bay, about 270 kilometres southeast of Scarborough Shoal.

"It would be naive for anyone to think this is just an ordinary joint exercise in the light of some assertive actions by China in the South China Sea," Wilfrido Villacorta, an international relations lecturer at the Manila-based De La Salle University, told AFP.

He described this as a "natural reaction" by the Philippines after recent "provocations".

Villacorta cited in particular China's recent flurry of reclamation activities on reefs in the Philippine-claimed Spratlys archipelago, turning them into islands capable of hosting significant military outposts.

China has repeatedly rejected allegations it is breaking international law in the South China Sea, insisting it has sovereign rights to the waters.

China hit out at the Philippines again on Tuesday, as it reasserted its rights to the Spratlys, which it calls the Nansha islands.

"The Chinese side is firmly opposed to the Philippines' occupation of some of the maritime features of China's Nansha islands by force," foreign ministry spokeswoman Hua Chunying told reporters in Beijing.

"Facts have proven once again that the Philippines is the real rule breaker and troublemaker."

Security analysts said Japan's decision to deploy warships into the South China Sea for the exercises, part of a broader trend to give military support to the Philippines, would anger China.

Chinese foreign ministry spokeswoman Hua said the exercises were being "closely" followed, describing them as "hyping up tensions".

China and Japan are separately engaged in a bitter and longstanding row over ownership of a Japanese-controlled island chain in the East China Sea. They are known as Diaoyu in China and Senkaku in Japan.