High-speed winds and lightning devastated many villages, bringing down homes and leaving dozens injured.
The northern state of Uttar Pradesh reported the highest death toll - 38. More than 70 people had died in dust storms in the state earlier in May.
Officials told BBC Hindi that casualties could go up further.
Twelve people were reported dead in the southern state of Andhra Pradesh, which was also severely hit by the storms. Nine people were killed in the eastern state of West Bengal, while two people have been confirmed dead in Delhi.
All four states remain on high alert as officials warn of more thunderstorms over the next few days.
"The danger is not yet over," Uttar Pradesh's relief commissioner Sanjay Kumar told BBC Hindi.
India's Meteorological Department had issued a warning on Sunday before the storms hit, warning people to stay within their homes. Wind speeds were around 109 km/h (67mph) accompanied by thunder and lightning, officials said.
Air travel in Delhi was also affected, with around 70 flights being diverted from the city's international airport on Sunday night.
Prime Minister Narendra Modi said on Twitter that he "prayed" for the speedy recovery of those who were injured and he asked officials to provide assistance.
Mr Kumar told BBC Hindi that more than 30 people had also been injured in Uttar Pradesh.
He added that many of those who had died had been killed as their homes collapsed amid heavy winds and lightning. He said that the relief department is assessing the damage in the state.
Large parts of India have been struck by deadly storms in the past month. More than a 100 people died in northern India on 4 May due to intense dust storms and heavy rains.
Authorities at the time said they were shocked by the ferocity of the storms, adding that it was one of the worst they had seen.
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