It had posted a net loss of Rs 5.11 crore in the year ago period, the company said in a regulatory filing.
Income from operations fell to Rs 545.45 crore in the fourth quarter of 2016-17 from Rs 807.44 crore in the corresponding period of the previous year.
During the full 2016-17 fiscal, the company posted a net profit of Rs 19.41 crore against a net loss of Rs 240.12 crore in 2015-16.
Income from operations fell to Rs 2,502.14 crore last fiscal from Rs 2,982.07 crore in 2015-16.
The Zuari-group controlled MCFL has a urea plant near Mangalore port with an annual capacity of about four lakh tonnes three lakh tonnes of phosphatic fertilisers.
Saroj Poddar-led Zuari group has 53 per cent stake in the company, while Vijay Mallya's UB group has 22 per cent shareholding.