Mr Singh will hold talks with his Japanese counterpart Shinzo Abe on a wide spectrum of issues of mutual interest and discuss ways to bolster strategic and global partnership between the two countries.
This is the postponed annual summit between the two Prime Ministers which was originally scheduled for November last year. The visit was deferred in view of the announcement of general elections in December last year.
National Security Advisor Shivshankar Menon, Pulok Chatterjee, Principal Secretary to Prime Minister, and other senior officials are accompanying Mr Singh.
Negotiations for the civil nuclear cooperation agreement have not made much headway since Japan was struck by Fukushima nuclear disaster in March, 2011.
"Agreements always take a certain amount of time... Discussions have been given some impetus recently but there are a number of stages we will have to go through before we reach the signature. I cannot put a date on it but we would certainly like to progress," Foreign Secretary Ranjan Mathai said in an indication that several issues still need to be worked out.
"We hope to make by the end of this year more progress in this field," he said.
On whether India has raised issues of nuclear safety during its discussions with Japan, he said, "Safety is one of the issues which we always discuss whenever we have discussions on civil nuclear cooperation with any country.
"And in the present atmosphere, safety is in fact probably a very high priority in our bilateral cooperation with any country. Certainly, with the Japanese, we will be discussing this at great length," he said.
Japanese officials have affirmed that Tokyo is committed to the nuclear cooperation pact notwithstanding its strong concerns over nuclear safety.
The two Prime Ministers will take stock of the India-Japan Strategic and Global Partnership and discuss how to further strengthen it. The two leaders are expected to review the entire gamut of bilateral relations including economic and defence cooperation and people-to-people ties.
On his way back from Tokyo, Mr Singh will visit Bangkok on May 30-31 aimed at elevating bilateral relations into a "strategic partnership" but the long-awaited Free Trade Agreement is unlikely to be inked with some issues still to be sorted out.
On Wednesday, the Prime Minister will call on Emperor Akihito and Empress Michiko, who will host a lunch for him.
The Emperor has accepted an invitation to visit India, dates for which are being worked out by the two sides.
Mr Singh will hold summit-level talks with the Japanese Premier the same day on the entire gamut of bilateral ties with special focus on giving a boost to cooperation in defence, economic, energy and other areas.
The Prime Minister will be highlighting greater investment opportunities in India and seek greater Japanese private sector investments. We see very good prospects for increasing Japanese investments in India," Mathai said.
The two leaders will also discuss regional and international issues including Afghanistan.
They will review major projects such as the Delhi-Mumbai Industrial Corridor, the Western Dedicated Freight Corridor, and the infrastructure upgrading process in the Chennai-Bangalore corridor.
Referring to defence cooperation, Mathai said India has invited Japan to hold naval exercises in the Indian Ocean.
"We are going to institutionalise the regular exercises between the Indian and Japanese navies," he said.
The Prime Minister's hectic schedule in Tokyo will start on Tuesday with Japanese ministers for Foreign Affairs and Economy, Trade and Industry calling on him.
Mr Singh's visit to Bangkok will be the first in nine years after the 2004 visit by the then Prime Minister Atal Bihari Vajpayee.
Geo-politics, the trilateral highway project involving India, Thailand and Myanmar, defence, science and technology, education and culture, are some of the issues which will be discussed by Mr Singh with his Thai counterpart Yingluck Shinawatra.
The process to ease the consular access and visa procedure and tourism related to the Buddhist circuit are also expected to be covered in the bilateral talks. Thailand is a Buddhist majority country.
The Prime Minister returns to Delhi from Bangkok on May 31.