The leaders were discussing increasing exchanges of top diplomats and defence officials and closer coastguard cooperation, finalising a three-day special summit between Japan and the Association of Southeast Asian Nations (Asean), officials said.
Tokyo Saturday pledged $20 billion in aid and loans to Southeast Asia at the summit with leaders of the Asean regional bloc, the latest step in its bid to woo global public opinion in its territorial dispute with China
In bilateral talks Sunday, Japan and Myanmar also agreed on an investment accord to accelerate Japanese investment in the former junta-ruled country, while Tokyo and Laos agreed to kick-start talks on a civil aviation agreement, officials said.
The talks came a day after Japan and Asean agreed on the importance of the "freedom of overflight and civil aviation safety", seen as a mild regional rebuke to China for its unilateral declaration last month of an Air Defence Identification Zone (ADIZ).
China denounced as "slanderous" remarks by Japanese Prime Minister Shinzo Abe at the summit calling for Beijing to rescind its air zone, which was widely criticised as increasing regional tensions.
Beijing has said all aircraft entering the zone have to submit flight plans and obey orders issued by Chinese authorities.
Some analysts fear the ADIZ in the East China Sea is a forerunner to a similar zone in the South China Sea, which Beijing claims almost in its entirety.
China has sovereignty disputes with four members of Asean -- the Philippines, Vietnam, Malaysia and Brunei -- and has been repeatedly accused of intimidation and coercion.
"We will continue to provide support, both at the public and private level, for infrastructure building initiatives and work toward Myanmar's development," Abe said after meeting with Myanmar's President Thein Sein.
In addition to Tokyo's development aid in loans, the investment accord signed Sunday would likely boost Japanese investment in the quickly developing former pariah state, a trade ministry spokesman said.
The deal would give Japanese companies so-called national treatment, or rights that local businesses receive in Myanmar when making investment decisions, helping Japanese firms avoid political risks in investing there.
The move comes as Myanmar prepares for an economic resurgence following the end of decades of military rule, which in turn is attracting attention from firms all over Asia and the West.
Meanwhile, Abe and Laotian Prime Minister Thongsing Thammavong agreed to start negotiations for a civil aviation agreement that would pave the way for direct flights between Laos and Japan, officials said.
They also agreed to continue their talks to launch a bilateral security dialogue framework involving foreign and defence officials, according to Japanese officials.
With Vietnam's Prime Minister Nguyen Tan Dung, Abe discussed strengthening cooperation between the coastguards of the two countries which both face territorial disputes with Beijing in the South China Sea or in the East China Sea.
In bilateral talks with Vietnam, Laos and Myanmar, Abe took up the issue of China's air defence zone, Jiji Press reported, without citing sources.
Dung said the issue should be resolved based on international law while Thongsing said it was important to settle it by peaceful means, Jiji said.
With Cambodia, whose economy is heavily reliant on China, Japan is also expected to discuss an aviation treaty and further exchanges of defence officials, officials have said.
The Japan-Asean summit commemorating 40 years of ties with the bloc comes at a time Tokyo is keen to garner support in its fractious spat with Beijing over the sovereignty of a small chain of islands in the East China Sea.
The case has taken on a greater urgency since China's declaration of the air zone which covers the contested archipelago.