Paddy, the primary crop of the kharif season, is likely to be hit as June as well as July are expected to be rain-deficit. The output of pulses such as arhar (pigeon pea), soybean and coarse cereals is also likely to be affected.
As droughts occurred in patches across the country, there won't be a disastrous impact on the overall food-grain production but it may have beating on small and marginal farmers by way of breaching their income security.
"The areas with irrigation such as Punjab and Haryana are not of concern. The real challenge will be looking at the income security of small and marginal farmers in rain-fed areas," said T. Nandkumar, former Union Agriculture Secretary.
A senior official at the Agriculture Ministry said that it was in constant touch with the states to apprise the Centre of the developing situation.
"We have asked them to be prepared with precautionary and remedial measures in case there is deficit rainfall," said the official, requesting anonymity.
However, there was no clarity if the state governments have ensured optimum seed reserves if first sowing attempt goes waste due to erratic rainfall.
The Food Ministry has started procuring over 50,000 tonnes of onion to deal with shortage if output goes down, indicating the government is not optimistic about good rainfall this year.
Farmers have been advised by private weather forecaster Skymet to postpone sowing by almost a week of the conventional dates as it said there are less chances of rains if the onset of the monsoon is delayed.
If there is a long gap between two rain spells, there is high probability of newly planted seeds getting killed.
Skymet has predicted "below average" monsoon 93 per cent of LPA this year with indications of higher risk in the eastern parts and major portion of Central India being rain deficient.
The average, or normal, rainfall in the country is defined between 96 and 104 per cent of a 50-year average for the entire four-month monsoon season, or Long Period Average (LPA), which is 887 mm.
Meanwhile, the India Meteorological Department (IMD) has predicted "near normal" monsoon 95 per cent of the LPA with evenly distributed rainfall.
It, however, said there is 51 per cent chance that the monsoon would be normal or above while there is 49 per cent probability that it remains below normal.
The Agriculture Ministry official said the rainfall this time is expected to be "erratic" and "sluggish" citing recent developments related to the monsoon.
The second half of the rainy season would see better rainfall as August and September are expected to see normal rains. However, the entire season is expected to end on a deficit note.
The rainfall in June will be 77 per cent (164 mm) of the LPA while it will be 91 per cent (289 mm) in July, 102 per cent (261 mm) in August and 99 per cent (173 mm) in September, as per Skymet.
Skymet has said that paddy production is expected to reduce to 97.78 million tonnes this kharif season compared to 101.96 million tonnes in the previous season.
It also said there is 40 per cent possibility of about 66 per cent districts in the country being deficient or largely deficient if the monsoon is "below normal".
Nandkumar expects about 100 districts, including those in Maharashtra's Vidarbha region, Telangana, Bihar and Jharkhand, to be rain deficient.
(Saurabh Katkurwar can be contacted at saurabh.k@.in)
( With inputs from IANS )