The 59-year-old critical care specialist was suffering from brain cancer since 2014, hospital officials said.
Dr Maitra was being treated at the superspeciality Belle Vue Clinic where he used to practise also.
He was admitted to the hospital on Monday after his situation deteriorated and breathed his last in the afternoon.
The doctor leaves behind his wife, two sons and a daughter.
One of the leading doctors in the city, the cardiologist had handled many VIP patients like screen goddess Suchitra Sen, West Bengal Chief Minister Mamata Banerjee and Swami Ranganathanandaji, former president of the Ramakrishna Math and Mission.
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The chief minister condoled his death saying it a big
loss to the healthcare system in the state.
"Shocked to hear about the death of Dr Subrata Moitra. He was a personal friend and asset to us. A great loss to healthcare sector in Bengal," she tweeted.