The meeting took place on the sidelines of the annual summit of the 10-nation ASEAN grouping which is being attended by a number of its dialogue partners including India, China, Japan, the US and Australia.
"Meeting a valued friend and a trusted partner. PM @narendramodi and PM @AbeShinzo held a wide ranging and engaging discussion on intensifying special strategic and global partnership between the two countries," external affairs ministry spokesperson Raveesh Kumar tweeted along with photographs of the meeting.
PM Modi and Shinzo Abe's meeting came two days after officials of India, the US, Japan and Australia held their first meeting to give shape to the much talked about quadrilateral alliance to keep the Indo-Pacific region "free and open".
Japan's Foreign Minister Taro Kono last month had said that Tokyo favours the quadrilateral dialogue to further boost strategic partnership among the four countries.
PM Modi also held a bilateral meeting with Sultan Hassanal Bolkiah of Brunei focus of which was expanding cooperation in areas of trade, investment and renewable energy.
"PM @narendramodi met with Sultan Hassanal Bolkiah of Brunei Darussalam. Both leaders had fruitful discussions on expanding bilateral partnership, specially in trade and investment, renewable energy, culture and people to people contacts," Mr Kumar tweeted.