Abe - in Indonesia on a regional tour that has taken in Australia and the Philippines and will include Vietnam - said their two island nations gave maritime cooperation the "highest priority".
"Japan will actively encourage cooperation on maritime security and encourage the development of the remote islands of Indonesia," he said through a translator at the presidential palace in Bogor.
Last month Tokyo and Jakarta unveiled an agreement aimed in part at strengthening Indonesia's ability to defend its vast marine borders.
Indonesia has vowed to protect its sovereignty from intrusions by fishing vessels, and has blown up foreign boats in a show of force, including some from China.
Japan, which has a territorial row with China over disputed islands in the East China Sea, has worked to strengthen ties with members of the Association of Southeast Asian Nations such as Indonesia.
The defence and foreign ministers of Japan and Indonesia will meet this year to discuss deepening "cooperation in the fields of defence and security", Abe added.
Widodo said Japanese investment in Indonesia had nearly doubled from 2015 to almost USD 5 billion last year. The two leaders discussed opportunities centred on large infrastructure projects including a medium-speed rail line and key port.
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