Beijing on Wednesday questioned the motive behind Manila's extraordinary protest against an incident that happened more than a month ago involving Chinese coast guard vessels and a water cannon in the South China Sea.

Foreign Ministry spokeswoman Hua Chunying reaffirmed China's stance that Beijing does not accept the protests or representations of the incident from the Philippines.

"There are a large number of Filipino fishing boats frequently appearing in the waters near Huangyan Island. Some of them were not there for fishing but were trying to remain illegally in the waters. All of those movements are obviously organized and confrontational, so China has plenty of reasons to doubt Manila's real purpose," Hua said.

The Philippines protested on Tuesday against the Chinese coast guard vessel's use of a water cannon on Filipino fishermen near the disputed waters in late January, according to Reuters.

Philippine President Benigno Aquino III said clarification of the incident would be sought from Beijing.

"We are not sure, at this point, if we can call it their standard operating procedure," he said.

Hua emphasized that China has maintained the utmost restraint in facing the seriously provocative behavior and has taken minimal measures.

"What concerns China most is that the Philippines enhanced its harassment in the South China Sea and seized seven Chinese fishing boats. What they are doing is like a thief crying ‘Stop thief!'" she added.

"The Chinese government will never tolerate these deliberate provocations," said Hua, who also urged Manila to correct the wrongs, respect Chinese sovereignty and stop generating more issues.

On Nov 29, the legislature of China's Hainan province approved a requirement that foreign fishing boats and foreigners must obtain permission under the authorities of the State Council to fish or carry out fishery resource surveys within waters administered by China's southernmost island province. The regulation took effect in January.

Li Guoqiang, a researcher of Southeast Asian studies at the Chinese Academy of Social Sciences, said Manila's protest was nonsense.

"Before asking the Chinese government to explain the use of a water cannon, the Philippines should explain the reason their so-called fishing boats were entering Chinese sovereign waters," he said.

The Philippines has made claims in the South China Sea and wants to increase its presence in the region, even though Huangyan Island and its waters are actually controlled by China, Li said.

"Their provocation is not only a way to continue their illegal claims on the waters, but also a means to gain sympathy from the international community," he added. "Manila's high-profile actions are quite possibly supported by some major countries that do not have direct interests in the region, such as the United States and Japan."