The Director-General of Health, Chai Chuah, says he is stepping down early from the job.
Mr Chuah made the announcement a short time ago, adding his last day on the job will be February the second next year.
He said it has been his view that the health system needs to tackle the challenges ahead as one team.
Mr Chuah has commented that while significant progress has been made in shifting the system forward, it has not been without controversy.
In August, he apologised to the then government for a $38 million funding allocation blunder.
As Director-General of Health, he said he fully owned the error and he accepted the recommendations of an independent report.
"I have apologised to the Minister of Health and the health sector for the error and provided an undertaking that we will learn from this and fix it," he said.
The new Minister of Health, David Clark, would not comment.
Executive director of the Association of Salaried Medical Specialists Ian Powell said the resignation came as no surprise.
"It has become increasingly clear for a while now ... the relationship with the Ministry, or at least parts of the Mininistry of Health, and District Health Boards - at the very least but also other organisations as well - has not been good and it's hard for the system to function."
Dr Clark said he was advised by the State Services Commission that an acting director-general will be appointed shortly.