MANILA - The presence of more than 200 Chinese fishing boats near an island occupied by Manila in the disputed South China Sea is illegal and a clear violation of Philippine sovereignty, the country's foreign ministry said on Thursday.

"Such actions when not repudiated by the Chinese government are deemed to have been adopted by it," the Department of Foreign Affairs said in a rare rebuke of Beijing.

President Rodrigo Duterte has pursued warmer ties with China since taking office in 2016 in exchange for billions of dollars of pledged loans and investment. He said this week China just wants to be friends with the Philippines.

"I was given arms and ammunition and until now they have not asked anything, they have not asked for any territory," Duterte said on Tuesday.

The presence of the trawlers near Thitu island raised questions about their intent and role "in support of coercive objectives," the ministry said, days after the Philippines lodged a diplomatic protest with China.

The Philippines has monitored more than 200 Chinese boats near Thitu, also known as Pagasa in the Philippines, from January to March this year, according to military data.

"These are suspected maritime militia," Capt. Jason Ramon, spokesman for the military's Western Command said this week.

"There are times when they are just there without conducting fishing. At times, they are just stationary."

The Philippines, Brunei, China, Malaysia, Taiwan and Vietnam have competing claims of sovereignty in the busy South China Sea, a conduit for goods in excess of $3.4 trillion every year.

"We call on concerned parties to desist from any action and activity that contravenes the ASEAN-China Declaration on the Conduct of Parties in the South China Sea, as these generate tension, mistrust and uncertainty, and threatens regional peace and stability," the ministry said.

In Beijing, Foreign Ministry spokesman Geng Shuang did not refer directly to Manila's protest, but he said bilateral talks on the South China Sea held in the Philippines on Wednesday were "frank, friendly and constructive".

Both sides reiterated that South China Sea issues should be resolved peacefully by parties directly involved, he said.

Last month, U.S. Secretary of State Mike Pompeo assured the Philippines it would come to its defense if it came under attack in the South China Sea.

(Additional reporting by Michael Martina in Beijing Editing by Clarence Fernandez and Darren Schuettler) ((karen.lema@thomsonreuters.com; +632 841-8938; Reuters Messaging: karen.lema.thomsonreuters.com@reuters.net))