Fonterra chairman John Wilson's decision to step down after a serious health scare has come as a shock to the industry.

The dairy cooperative announced this morning that Wilson will remain a director on its board until its annual meeting in November, when he will retire from the board.

The company said in a statement that Wilson had undergone a significant surgery within the last month and would require ongoing treatment.

Wilson was up for re-election in this year's Fonterra director elections, which closed on Monday.

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Existing director John Monaghan will be the new chairman. He has been on the board of Fonterra since 2008.

Wilson said the decision to stand down as chair had been difficult but was ultimately in the best interests of the cooperative.

"I have made a very good recovery and am well but will need on-going treatment.

"It has been a privilege to serve you as chairman and give something back to this great cooperative that continues to give my family and me so much.

"As many of you will know from experience, governance roles are incredibly rewarding, but equally demanding on the individual and their families.

"Continuing as chairman when I cannot put my full energy and attention into the role is not appropriate."

Monaghan grew up on a dairy farm and has current farming interests in the Wairarapa and Otago.

During his time on the Fonterra Board Monaghan has served on multiple committees, chairing several of them, Fonterra said.

He has been closely involved in the process to appoint a new chief executive to replace the outgoing Theo Spierings and will now lead the advancement of this appointment.

Shareholder response

Learning Fonterra chairman Wilson was stepping down for health reasons came as a surprise and a shock to the leader of the big dairy cooperative's shareholder council.

Council chairman Duncan Coull said he learned yesterday from Wilson that he had stood down.

"I was very surprised....and it was a shock. My thoughts go out to John and his family. He's in good spirits and I thank him on behalf of farmers for 17 years of service to our farmer-owned cooperative," said Coull, who represent's Fonterra's 10,000-odd shareholders.

"In my short time in this cooperative, I don't know of anyone else who has given that much to the co-op. So there's huge gratitude on behalf of farmers."

Coull did not know that Wilson had undergone "significant" surgery, according to a statement from Fonterra today.