The head of Capital and Coast Health (CCDHB) has announced she will stand down at the end of the year, saying it is time for a new challenge.

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Debbie Chin took over as interim head of the CCDHB in 2013 and was appointed as permanent chief executive in 2015.

Previously she had been involved in key health sector roles for more than two decades, including being a Prime Ministerial advisor and a period as Acting Director General of Health.

Mrs Chin said the highlight of her time at the Capital and Coast DHB has been the amazing staff, who have shown incredible dedication and commitment to their patients.

The Wellington health board has struggled with debt, but Mrs Chin said she had grasped opportunities to deliver more and better services to patients in the last few years.

"For example, building a $15 million youth forensic unit, which will cater to young people from around the country, a new dialysis unit at Kenepuru [Hospital in Porirua].

"[We have also] recently spent a lot on new radiology equipment, including MRI and CT scanners."

The Nurses Organisation has praised Debbie Chin's leadership and she said she had always valued the support she had from it and other health sector unions.

The union is concerned about her resignation and said it should ring alarm bells for Treasury and the government.

In a statement the organisation's chief executive, Memo Musa, said Mrs Chin was the fourth chief executive to resign from the CCDHB because of long-term underfunding.

"We are actually shocked and disappointed that the impossible task of running a DHB, providing good services to the community of Wellington as well as other DHBs in the central region, without enough funds, has taken another head."

The Nurses Organisation's Wellington organiser, Georgia Choveaux, said Debbie Chin had been a wonderful leader at the CCDHB, and had allowed clinicians to make patient decisions, rather than accountants.

She said debt problems at the board had arisen from the poor funding model, rather than anything the outgoing chief executive had done.

"Capital and Coast has one of the most efficient and effective public health services in the country. They have one of the lowest rates of patient stays, one of the most efficient and cost effective work forces of any tertiary hospital and yet they are constantly stuck in debt.

"You can only conclude that it is the funding model, which gives [Wellington] the lowest per capita funding of any DHB, that's the real problem."

The chairman of the health board, Andrew Blair, has thanked Mrs Chin for her hard work and dedication and her agreement to work with the board to ensure a smooth transition.