States like Gujarat and Rajasthan have over 80 per cent of deficient rain.
The respite is that monsoon is likely to revive in the first week of July and rain is expected in the national capital and northwest plains from July 5, the agency added.
"As of now, the national cumulative average monsoon rain is deficient by a whopping 42 per cent, making it only the 12th instance in last 113 years when rainfall deficit has been over 30 per cent in the month," Skymet, a private forecasting agency said.
"The Northern Limit of Monsoon (NLM) continues to pass through Veraval, Surat, Nashik, Wasim, Damoh and Sultanpur. The western arm, passing through Veraval, Surat and Nasik has been stagnant for the 13th consecutive day," it said.
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According to the Indian Meteorological Department (IMD), the rainfall in the country has made marginal progress as compared to last week. It received 74.4 mm of rainfall from June 1 to June 25, as compared to normal precipitation of 124.5 mm, which is 40 per cent less.
Central and northwest India continued to receive less rainfall from June 1 to June 25. Northwest India received 25.0 mm of rainfall as compared to normal rainfall of 48.3, which is 48 per cent less while central India received 51.4 mm as compared to normal rainfall of 118.9 mm, which is 57 per cent less.
"A fresh western disturbance would affect northwest India in the beginning of July. We are expecting mild interaction of monsoon and western disturbance and this will help in advancement of monsoon in Northern Uttar Pradesh, Himachal Pradesh and Jammu division," B P Yadav, Director, IMD.