The rainfall was 14 per cent lower than normal in the June-September monsoon season, provisional data posted on the website of Indian Metrological Department (IMD) showed on Wednesday.
The IMD office had forecast a 12 per cent rain deficit in the four-month long season.
That makes this the first back-to-back drought in three decades, and only the fourth in more than a century. The scant rains have hit the yields of summer-sown crops, especially in the south of the country.
Monsoon rains have been below average levels due to El Nino, a weather pattern caused by Pacific Ocean warming that can lead to droughts in South Asia.
In some regions the rainfall deficit during the season was as high as 47 per cent, resulting in shortages of drinking water.