At least 54 people died in a district in the northern Indian state of Uttar Pradesh over the last few days, the Times of India newspaper reported on Monday, as authorities probed if the loss of lives was due to the heatwave in the region.
Another 45 people died in neighbouring Bihar state, local newspapers reported.
The Indian Meteorological Department (IMD) issued a red alert warning last week for extreme heat in some regions of the country, including Uttar Pradesh and Bihar.
The government said it was investigating the cause of the deaths that occurred over three days last week in Uttar Pradesh's Ballia district, about 970 km (600 miles) southeast of New Delhi.
"A few of the deaths are related to old age, while some have different reasons. There is no concrete evidence of heatwave behind these deaths."
The government fired Diwakar Singh, the chief medical official at the main state hospital in Ballia, for saying that the deaths were due to heat.
The state's deputy chief minister, Brajesh Pathak, said on social media that Singh had been removed from his position for making an "irresponsible statement."
Temperatures have soared close to 45 degrees Celsius (113 degrees Fahrenheit) in recent days in Ballia with a severe power crisis compounding the situation.
In Bihar, 45 people lost their lives due to heat-related illnesses, the Hindustan Times newspaper reported. Officials in Patna, the capital of Bihar, did not answer phone calls.
While the heatwave was expected to continue in some regions on Monday, parts of India's northeastern Assam state reeled under floods triggered by heavy rains.
"Rainfall intensity in Assam and other northeastern states is likely to rise this week. Many pockets are expected to receive heavy to extremely heavy rainfall this week, which could lead to flooding," said a senior official with the IMD.