However, rice production may not be hit with rainfall in eastern Indian being better so far and north India having irrigation facilities, he added.
The monsoon, which is the main source of water for 60 per cent of arable land, was 43 per cent below average in June. The rainfall deficit was the highest in Central India.
"There will be impact on production of cotton, soyabean and groundnut because of poor rains in some states like Gujarat," Indian Agricultural Research Institute (IARI) Director H S Gupta told reporters.
On rice, Gupta said that production of the key staple may not be affected as the northeastern region has received good rains so far and the entire north is irrigated.
As per official data, area sown to cotton was down by 47 per cent at 45.2 lakh hectares till last week of the Kharif season, while oilseeds comprising majority soyabean was lower by 88 per cent to 22.16 lakh hectares.
Sowing of kharif (summer) crops like rice begins with the onset of southwest monsoon from June, while harvesting from November onwards.
Last year, cotton output was a record at 36.5 million bales, while soyabean and groundnut output was 11.94 million tonnes and 7.65 million tonnes, respectively, in the kharif season. Kharif rice production stood at 92.01 million tonnes.
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