"Matter of joy & pride that Japan has conferred Dr. Manmohan Singh with Grand Cordon of the Order of the Paulownia Flowers. Congrats to him," said Modi.
Singh was today conferred with the award, one of Japan's top national awards, becoming the first Indian to receive the rare honour.
The 82-year-old former Prime Minister was presented the award 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.
He is among 57 foreign recipients named for the 2014 Autumn Imperial Decorations.
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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".
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".