The senior doctors' union says David Meates was put in an "untenable position" after the head of the Canterbury and West Coast District Health Boards resigned.
Mr Meates had been at the helm for more than a decade - through the Christchurch and Kaikoura quakes and the 2019 terrorist attack.
His departure comes as Canterbury DHB faces a nearly $180 million deficit.
Mr Meates has not outlined his reasons for leaving and the Canterbury DHB has thanked him for his service.
He's the third member of the executive leadership team to resign in the past month.
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