Synlait Milk's chief executive Leon Clement will step down at the end of the month, the company announced on Monday.
John Penno, the company's co-founder and former chief executive, will fill the role until a permanent replacement is found.
Clement has been chief executive at the company since September 2018, and the company's board said it was "with regret" it had accepted his resignation.
"Leon has been an authentic and transformational leader," the company's chair Graeme Milne said.
"He has successfully repositioned Synlait’s purpose, ambition, and strategy to make us a more diversified and sustainable company."
Clement said it had been a privilege to lead the company.
"It has been an intensive period of change and growth and I am proud of our achievements. Synlait has an amazing team that is making a positive and sustainable impact in the areas we operate."
Last month Synlait announced its first-half profit had dropped 76 percent, to $6.4 million, after COVID-19 had led a decrease in demand for the infant formula it produces for the A2 Milk Company, its largest customer.
In its statement on Monday the board said it "recognises the substantial impact that COVID-19 has had on Synlait and the difficult challenge this would present to any management team".