The 86-year-old was bedridden for the last five to six months and had stopped eating.
He breathed his last around 8.10 pm this evening, a family member told PTI.
Dutta is survived by his son Ashish and daughter Anita.
A midfielder, who represented India at the 1954 Asian Games, the former Mohun Bagan and East Bengal footballer later made a name for himself as a tactical genius as he pioneered professional coaching in India.
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"He was an institution in himself. We shall miss you. May his soul rest in peace," Mohun Bagan said in its homage.
Legendary footballer P K Banerjee who played alongside Dutta in the Indian team described him as a "true fighter".
"He took sport to a different level during his playing days at East Bengal, Mohun Bagan and India. He fought till the end," Banerjee said.
Four years after his return, Dutta got his first big break when he took over as East Bengal's coach in 1963, midway through the Calcutta League. He managed the club till 1964.
He quit his job to become a full time coach, thus becoming India's first professional coach and was the technical director of Indian team for the Nehru Cup in 1987.
In a condolence message, West Bengal Chief Minister Mamata Banerjee wrote on twitter: "Saddened at the passing away of Amal Dutta. Football world will miss him. It's a great loss. My condolences to his family and friends.