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.
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.
Tea estate managers in India's Assam state will be charged with manslaughter if more labourers die of water-borne diseases, officials have warned.
They made the announcement after a sudden rise in the number of workers who have died from diarrhoea and other water-borne diseases.
Officials say 168 people - mostly tea workers - have died over five months.
The state government's order says that if more die, proceedings will be initiated under the Indian penal code.
Assam Health Minister Himanta Biswa Sarmah said the "extreme step" had been taken because tea estates were doing nothing to provide safe drinking water to their labourers.
Assam is India's largest tea-producing state, with more than 800 estates employing tens of thousands of labourers.
"The tea gardens have the resources but despite repeated requests, they have done nothing to provide their labourers with safe drinking water. So the government is compelled to take tough measures," Mr Biswa Sarmah said.
He said his government was prepared to help the tea gardens install safe drinking water sources - like tube wells - from funds meant for other projects.
The Indian Tea Association (ITA) has reacted sharply to the executive order. An ITA spokesman said the government's order was based on "funny logic".
"By this yardstick, a city's mayor could also be charged with manslaughter if someone dies by drinking contaminated water," he said.
But the Assam health minister says officials of his department and those from the UN Children's Fund have toured diarrhoea-affected districts of the state and found that most deaths in tea gardens were easily preventable.
"In many gardens, tube wells existed by the side of open drains. In some, there was just one tube well for four or five labour colonies. And the deaths were happening in these gardens where the water source was unsafe," Mr Biswa Sarmah said.
He said that most of the deaths occurred in Jorhat, Golaghat, Moregaon and Dhubri districts.
But opposition parties in Assam described the government's move as a "gimmick" to absolve itself of the responsibility for the diarrhoea deaths.
"We have been asking the government to take appropriate measures since the deaths were first reported in April. The government has only woken up now," said Apurba Bhattacharya, spokesman of the opposition Asom Gana Parishad.
Members of the state's powerful All Assam Students Union (AASU) held demonstrations on Tuesday in front of government offices across Assam to protest against the deaths.
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