Japanese Prime Minister Suga Yoshihide and President Joko Widodo have called for continued cooperation on matters including health, security and the economy.
After the summit meeting, the leaders held a news conference.
Japan's new Prime Minister is on to the second leg of his inaugural trip abroad as the country's leader.
After leaving Vietnam, Suga Yoshihide has arrived in Indonesia where he is set to meet President Joko Widodo.
Japanese Prime Minister Suga Yoshihide is heading for Jakarta for talks with Indonesian President Joko Widodo.
Suga left Hanoi on Tuesday morning local time after he met with Vietnamese Prime Minister Nguyen Xuan Phuc the day before and delivered a speech on foreign policy.
Japan's Prime Minister Suga Yoshihide has left for Vietnam and Indonesia on his first overseas tour since assuming office.
During the four-day tour, Suga is scheduled to meet Vietnamese Prime Minister Nguyen Xuan Phuc and Indonesian President Joko Widodo. He will give a speech on Japan's policy towards ASEAN at a university in Hanoi on Monday.
Japan's Prime Minister Suga Yoshihide plans to visit Vietnam and Indonesia next week on his first trip abroad since assuming his post.
Government officials are arranging for Suga to meet Vietnamese Prime Minister Nguyen Xuan Phuc and Indonesian President Joko Widodo during his four-day trip, starting on Sunday.
NHK has learned Japan's Prime Minister Suga Yoshihide may visit Vietnam and Indonesia in mid-October if coronavirus situations allow. It would be his first overseas trip after taking office.
Recent infection curves have been relatively stable in the two nations. If Suga visits them, he is expected to meet Vietnamese Prime Minister Nguyen Xuan Phuc and Indonesian President Joko Widodo.
The foreign ministers of Japan and Indonesia have agreed to expedite preparations to hold a joint meeting of their foreign and defense ministers soon this year.
Japan's Foreign Minister Toshimitsu Motegi met Indonesia's Retno Marsudi in Jakarta on Friday. The two countries last held a so-called "two-plus-two" meeting in 2015.