The ties between India and Japan are on the upswing as both the countries have expanded mutual cooperation in diverse areas, including trade and commerce, in the last few years.
Various bilateral issues figure in the meeting between Emperor Akihito and Singh.
The Emperor and Empress Michiko had arrived here on Saturday on a six-day India trip.
In the morning, the Emperor was given a ceremonial reception at the Rashtrapati Bhavan.
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Singh had visited Japan in May when both sides had agreed to further enhance cooperation in diverse fields, particularly in trade and investment.
In the financial year 2011-12, India-Japan bilateral trade reached USD 18.43 billion. Japanese companies have an average annual investment to the tune of around USD 2-3 billion in the last few years.
The year 2012 marked the 60th anniversary of establishment of diplomatic relations between India and Japan.