In a BSE filing, the company informed that the resignation will be effective from June 30.
MCFL has a urea plant near Mangalore port with an annual capacity to produce about 4 lakh tonnes of urea and about 3 lakh tonnes of phosphatic fertilisers.
Zuari was competing with Pune-based Deepak Fertilisers for the takeover of MCFL since July, 2013, but the latter withdrew from the race and has been selling shares of MCFL through open market transactions since December, 2014.