Singh, who was India's prime minister for a decade till the 2014 elections, has been conferred the Grand Cordon of the Order of the Paulownia Flowers, one of the highest civilian honours of Japan. The award was conferred on Singh by the Japanese Emperor Akihito in Tokyo. Singh is the the first Indian to be conferred the honour.
The Japanese embassy said that Singh was being conferred the honour "in recognition of his significant contributions to the enhancement of relations and the promotion of friendship between Japan and India for about 35 years".
The award is expected to add lustre to Singh's legacy as prime minister at a trying time for his party. An MP of the Rajya Sabha, Singh has been largely away from the media space for the past six months following his Congress party's election debacle.
The award is also expected to bring into focus Singh's role in nurturing and fostering crucial international partnerships. The award has come weeks after Prime Minister Narendra Modi's much-trumpeted visit to Japan where warm chemistry between him and Japanese premier Shinzo Abe was on display.
Congress officials said Singh's relationship with Japan extends to several decades. They said that Singh, who was the finance minister in 1991 when the country had to be brought out of foreign exchange reserve crisis, had got promise from Japan of aid that helped the economy ride out the challenge.
Singh had said soon after the award was announced that he was "truly honoured".
"Japan's rise as a modern, knowledge-based industrial power has been a source of inspiration for India right from the time of our struggle for Independence," Singh had said.
In his message, Mukherjee said: "I am extremely happy to know that the Government of Japan has conferred one of its highest civilian honours -'The Grand Cordon of the Order of the Paulownia Flowers' upon you, making you the first Indian ever to receive this award."
"This important recognition is testimony to the immense service rendered by you over the years for the promotion of India-Japan relations and friendship," the president said.
Congress president Sonia Gandhi and her son and party vice-president Rahul Gandhi were among those who have congratulated Singh. Sonia Gandhi described Singh as a "statesman", saying the award "makes us, as indeed the entire nation, proud."