Mr Parrikar will undertake a two-day trip starting from March 30, the first foreign visit by an Indian Defence Minister since November 2013.
"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.
The last visit was undertaken by then Defence Minister AK Antony in November 2013, when he visited Russia.
Analysts point out that Mr Parrikar's choice of Japan for his first international visit is of strategic importance.
China, Japan's neighbour, has been perturbed by increasing India-Japanese ties besides increasing American interest in the region.
The thrust of Mr Parrikar's visit will be increasing defence cooperation and pushing the government's Make in India initiative.
Interestingly, the government is yet to take a final decision on a major defence deal for acquiring 12 amphibious aircraft-US2 from Japan.
The Defence Acquisition Committee, headed by Mr Parrikar, had sought additional information on the deal and hence, a final decision was not taken.
While a number of foreign defence ministers have visited India since the Modi Government took over, no trip has been organised by the Indian side so far.
While interim Defence Minister Arun Jaitley was scheduled to visit US last year, his visit was put off due to health issues.
Mr Parrikar is likely to undertake a number of visits soon.