Parrikar will undertake the two-day trip starting from March 30, first foreign visit by an Indian Defence Minister since November 2013, as part of the government's move to step up its defence diplomacy.
He is likely to visit South Korea after this trip.
"A number of requests have come from various countries and a visit by Indian Defence Minister was due for a very long time. Parrikar is going as part of defence diplomacy to strengthen our bonds," defence sources said.
Analysts point out that Parrikar's choice of Japan for his first international visit was of strategic importance.
China, Japan's neighbour, has been perturbed by increasing Indo-Japanese ties, besides increasing American interest in the region.
Thrust of Parrikar's visit would be on increasing defence cooperation and pushing the Modi government's 'Make in India' initiative.
Sources say one of the area of focus would be a major defence deal for acquiring 12 amphibious aircraft - US2 from Japan.
