Singh, 82, was presented 'The Grand Cordon of the Order of the Paulownia Flowers' by Japanese Emperor Akihito for his "significant contribution to the enhancement of relations and promotion of friendship" between Japan and India for about 35 years.
Emperor Akihito and Empress Michiko hosted a luncheon for Singh and his wife Gursharan at the Imperial Palace after the award ceremony, Kyodo News Agency reported.
"Manmohan Singh is the first Indian recipient of this Order," the Japanese government had said while announcing the prestigious award.
Singh had earlier said he was truly honoured and felt "humbled by the love and affection showered upon me by the people and government of Japan."
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He said it had been his dream to see India-Japan relationship grow and prosper and "this is an objective towards which I have worked, not only in my tenure as the Prime Minister of India, but across the larger part of my career in public service".
Singh, who served as the Prime Minister for 10 years from 2004, said he was heartened to witness the transformation in India-Japan relations into a durable partnership.
"I have no doubt that with the common efforts and initiatives of the people of Japan and India, we will scale greater heights in our bilateral relationship in future," Singh said.
Singh, in a departure from protocol, had received the emperor and empress when they arrived in India for an official visit last year.