"Rainfall is likely to be below normal," Earth Sciences Minister Prithviraj Chavan said.
The minister said the 2009 monsoon rainfall would be 93 per cent of the long-term average, lower than an earlier forecast of 96 per cent.
The annual monsoon hit the southwestern state of Kerala on May 23, a week ahead of schedule, but its progress has gradually weakened, threatening to hit the country's farm output and impact the economy.
The four-month rainy season normally kicks off around June 1 and covers the entire country by mid-July.
With only 40 per cent of farmland irrigated, most of India's small farmers rely on the monsoon to water their crops. A good season of rains also boosts rural demand for a range of products and is a key factor in determining expansion in the larger economy.