Angry workers surrounded the bungalow at Kunapathar in Assam state late on Wednesday, following a two-week long dispute with the management.
Police said the incident happened after the management asked some workers to leave their accommodation.
More than half of India’s tea output comes from 800 tea estates in Assam.
Local official SS Meenakshi Sundaram said some 700 tea garden workers surrounded the manager’s bungalow on Wednesday evening and set it on fire. Two vehicles belonging to the manager were also torched.
The charred bodies of Mridul Kumar Bhattacharyya and his wife, Rita, were later recovered from the debris, Mr Sundaram said.
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Police have detained three workers in connection with the incident.
Officials said Mr Bhattacharyya and his workers had been locked in a dispute for the past two weeks.
They said Mr Bhattacharyya had also faced protests at another tea estate that he owned two years ago.
In that dispute, angry workers set fire to his tea factory near the state capital, Guwahati, after he had allegedly fired on a crowd that had gathered near his house to protest against a reported attack on a local woman.
Several incidents of attacks on tea executives by angry workers have been reported from Assam in recent years.