The company had clocked a net profit of Rs 1.2 crore in the same period last year, it said in a BSE filing.
Net income declined to Rs 978.3 crore in April-June of 2016-17, from Rs 1,555.7 crore a year ago.
"Due to significant reduction in the selling price of complex fertilisers and potash during the current quarter and subsequent to quarter-end, the company is expecting reduction claim of Rs 47.33 crore on account of stock lying with distribution chain," the company said in the filing.
In July, the Centre had announced a cut in maximum retail price (MRP) of di-ammonium phosphate (DAP) by Rs 2,500 to Rs 22,000 per tonne, muriate of potash (MoP) by Rs 5,000 to Rs 11,000 per tonne and NPK nutrients by Rs 1,000 per tonne.
Shares of the Goa-based company declined by 2.22 per cent to settle at Rs 185.05 on BSE today.