Japan Prime Minister Shinzo Abe is on a four-nation tour to shore up support against China's increasing presence.
The Japanese PM praised the Filipino leader's efforts in strengthening ties with China.
Japan is the biggest provider of aid towards the Philippines and its most important trade partner.
Japan has also suspends talks with South Korea on foreign currency swap.
Opposition politicians promised to nullify the deal should their party win the next presidential election.
The Interchange Association, Japan will now be re-named as the Japan-Taiwan Exchange Association.
Japanese Prime Minister Shinzo Abe should have first mended ties closer home, Chinese media said.
He was flanked by US president Barack Obama in Oahu, Hawaii.
Japanese prime minister's visit is seen as a message to Donald Trump and a warning to China
Prime Minister Abe will also meet US President Barack Obama following his visit to Pearl Harbor.
No deal is expected over the islands which Japan refers to as Northern Territories.
Japanese PM Shinzo Abe and Russian President Vladimir Putin are expected to meet on 15 and 16 December.
Japanese troops attacked and killed more than 2,400 people at the US Naval base in Hawaii in December 1941.
Follows Obama's visit to Hiroshima, the site of the US nuclear bomb attack on Japan in 1945.
PM Shinzo Abe has said he wants to discuss the issue candidly with Russian President Vladimir Putin.
Abe also invited Chinese Premier Li Keqiang to Japan to attend a trilateral summit with South Korea.
Twitter users have questioned whether Kushner and wife Ivanka Trump should have been present in the meetings.
Chinese paper says India will get closer to Japan but will not enter into a 'brotherhood relationship'.
Japan is said to be of the view that a victory for Donald Trump would lead to policy changes in Asia-Pacific.
Japan earlier agreed to provide multi-role response vessels and mid-sized coastguard ships to the Philippines.
Japan's government's says the UK's exit from the EU will 'a major disturbance to the world economy'.
Putin says he will talk to Japan's Shinzo Abe about finding a solution where neither of the parties would feel defeated or a loser.