MANILA -- The Philippines filed diplomatic protests against China over two incidents in disputed waters, President Rodrigo Duterte's chief security adviser said Wednesday.

Manila protested the passage of Chinese warships through Sibutu Strait in the Philippines' southern tip without prior clearance and the swarm of 113 Chinese vessels around Filipino-occupied Pag-asa Island, National Security Adviser Hermogenes Esperon said.

Manila has no record of Beijing seeking diplomatic clearance for the passage in Sibutu Strait, Esperon said. Defense Secretary Delfin Lorenzana first reported the movement last week, adding it happened 4 times since February.

"Customarily, lahat ng military vessels that pass through our territory ask for diplomatic clearance. Nagkataon na in our record (It just so happened that according to our record), we do not have it on record that China asked for diplomatic clearance," Esperon said.

(Customarily, all military vessels that pass through our territory ask for diplomatic clearance. It just so happened that in our record, we do not have it on record that China asked for diplomatic clearance.)

"Ang reason nila (Their reason) is the right of innocent passage in a usual sea lane. In a sense that is correct. But in our customs and traditions and agreement with other countries, we always advise the country for diplomatic clearance," he said.

He likened seeking diplomatic clearance to knocking on a door before entering: "Katok lang (just knock)," he said.

Esperon said he has sent a note verbale to Foreign Affairs Secretary Teodoro Locsin Jr. for submission to China to protest the swarm around Pag-asa Island on July 24.

Locsin, in a Twitter post, said he has filed the note verbale.

I did. I listen only to military intelligence; I distrust civilian sources of "misinformation." When it comes to national security, I am the thinking trigger; the finger is the Commander-in-Chief and the Armed Forces which are the protector of people & state. https://t.co/CwKBdJysR0

— Teddy Locsin Jr. (@teddyboylocsin) July 31, 2019

"I did. I listen only to military intelligence; I distrust civilian sources of 'misinformation.' When it comes to national security, I am the thinking trigger; the finger is the Commander-in-Chief and the Armed Forces which are the protector of people & state," he said.

Pag-asa (Thitu) is the largest Filipino-occupied island in the disputed Spratlys. Esperon said it was unclear why the Chinese ships were there.

The Chinese vessels have since left because of bad weather and sought refuge in Subi Reef – one of 7 Chinese man-made islands in the South China Sea. It is closest to Pag-asa Island and has its own runway.

Esperon shared recent photos from Pag-asa island, showing that as of Tuesday, only 1 China coast guard ship and 3 Chinese fishing vessels were there.

"Ngunit huwag kayong mabahala dahil as of now – kung noong July 25 ay hitik na hitik, ngayon ay parang nawala na yung mga fishing boat doon. Kahapon, wala na," he said.

(Don't worry, as of now -- if there were many ships on July 23, the Chinese fishing boats have disappeared there. There were none yesterday.)

Esperon said the Philippines continues to strengthen its position in the West Philippine Sea, adding that 5 lighthouses have already been put up, with 5 more in the way.

The Philippines will also have its own high-flying unmanned aerial vehicle with a direct access to satellite imagery to help in this effort.