The Chinese embassy in Manila has defended Beijing's controversial coastguard law as "domestic legislation" and said China would continue to seek a negotiated resolution with the Philippines over their disputes in the South China Sea.

"China Coast Guard is an administrative law enforcement agency. The formulation of the coastguard law is a normal domestic legislative activity of China," the embassy said on its Facebook account, late on Monday night.

"Enacting such a coastguard law is not unique to China, but a sovereign right to all," the statement continued. "Many countries have enacted similar legislation. It was the Philippine coastguard law of 2009 that established the (Philippine Coast Guard) as an armed and uniformed service. None of these laws have been seen as a threat of war."

The statement could be seen as Beijing's latest attempt to ease tensions with its Southeast Asian neighbor. The two countries are locked in a complicated territorial dispute over parts of the strategically important South China Sea.

China's latest coastguard laws - which explicitly authorize pre-emptive strikes against foreign vessels in waters "under China's jurisdiction" - raised alarm in the Philippines and other countries with claims in the South China Sea, when they came into effect on Monday.

The Philippines filed a diplomatic protest over the legislation, which foreign minister Teodoro Locsin called on Twitter "a verbal threat of war to any country that defies it". The law has also heightened concerns in Vietnam, Brunei and Malaysia that China could take a more aggressive approach in maritime disputes with its neighbors.

The Chinese mission also dismissed as "fabricated" local media reports that a Filipino fisherman, Larry Hugo, had been harassed by coastguard vessel 5103 near the Philippine-occupied Thitu Island - second largest in the Spratly archipelago which is also claimed by China, Taiwan and Vietnam.

"Some forces in the Philippines, either for their own political interests or out of prejudice towards China, have not only misinterpreted China's normal legislation, but also fabricated and spread relentlessly fake news such as 'China coastguard harassing Filipino fishermen', despite repeated denial from authorities concerned - including the Philippine armed forces - of such an improbable case," the statement said.

The Chinese embassy also sought to justify last week's incursion by the Jia Geng research ship, which entered Philippine waters without permission near Samar, the country's third largest island. The visit fuelled speculation in Manila that it was collecting data in the resource-rich waters.

The embassy said the Chinese scientific survey ship was "seeking humanitarian shelter in Philippine waters due to unfavourable weather and sea conditions in the Pacific where they are scheduled to conduct a research mission".

The Philippine Daily Inquirer reported on Sunday, citing a government source, that the Chinese vessel had sought clearance from the Philippine authorities on Saturday to drop anchor in Cabugao Bay from January 29 until Tuesday "due to weather and sea conditions" but the application was still pending at the time of publication.

The Philippine Coast Guard on Monday said the Chinese survey ship had left that afternoon.

Antonio Parlade, head of the Armed Forces of the Philippines Southern Luzon Command, also told local media that the ship had sought shelter up to Tuesday because of bad weather.

"They made the request while they were approaching," Parlade said, according to the Malaya Business Insight newspaper.

The same Chinese research vessel was seen in waters off the northwest of the Philippines in September. It said at the time it was taking shelter from bad weather and left three days later.

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