Unexpectedly heavy rains began lashing the area on Thursday, nearly two weeks ahead of the normal monsoon season, which usually covers the country from early July to September.
The first wave of floods hit the northeastern state of Assam, cutting off road and rail links. Six people who tried to cross a swollen river on bamboo rafts drowned.
The neighboring state of Arunachal Pradesh reported 19 deaths from landslides with dozens more feared dead as the Brahmaputra River broke its banks. Some 300 mud and thatch huts were also washed away along the banks of the Dikrong River in the state capital Itanagar.
Six people were killed by lightning in Lucknow, northern India, as heavy rains lashed the country's most populous state of Uttar Pradesh.
Troops have been deployed in the affected regions. Indian authorities have opened a total of 50 refugee camps for at least 40,000 people displaced by the disaster.