"As per provisional information available... the number of human lives lost is 1,258," the statement said, adding that 31 million people were affected by the deluge across the country.
This takes the death toll due to rains and flooding in South Asia to 1,631 with 282 deaths reported in Bangladesh and 91 in Nepal.
In India, large parts of northern Uttar Pradesh, eastern Bihar and northeastern Assam states are submerged, officials said.
Losses due to the floods across India have been estimated to be 12.68 billion rupees (313 million dollars), the home ministry statement said.
Logistical support provided by the federal government to the affected states includes deployment of army personnel, Indian Air Force helicopters for rescue and naval diving teams and boats, it added.