The country's biggest charity helping people dealing with rare disorders is upset the Government has gone back on what it says was a multi-million dollar pre-election pledge for rare diseases.

The NZ Organisation for Rare Disorders says it is stunned a $20 million pledge to establish a separate fund that would allow rare disease patients to access life-saving medicines would not go ahead.

However, the now Government says no such amount or policy was ever announced and that money would still be made available for people with rare disorders in other ways such as a pilot programme run by Pharmac.

Chief executive Dr Collette Bromhead said the organisation met with two Labour MPs last week where they were told that the $20m funding over four years would not be part of the upcoming Budget.

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It is understood that figure came up while Labour's then Health spokesman, now Health Minister, Dr David Clark spoke with rare disorder patients and families during the election. It was also reported by media outlets at the time.

Dr Bromhead said: "The decision to cancel the fund for medicines is a complete U-turn by the Government and has been done without any consultation with the rare disease community,'' she said.

"It leaves these vulnerable patients with no way to access the essential medicines that could extend their life and provide them with a better quality of living.''

Today Dr Clark told Newstalk ZB Labour made no specific commitment in terms of the coalition agreement when the Government was formed, but he had taken it upon himself to commit to coming up with a solution.

"I have made a personal commitment to ensuring that we find money for rare disorders. It was something I was concerned about in Opposition and I was concerned that Pharmac might not continue with the fund that it had set up."

Pharmac's funding medicines for rare disorders programme has seen four medicines approved in the last few years. The programme has made $5m available per year, for five years, to fund rare disorder medicines.

"I have now got assurance from Pharmac that it is going to continue with that fund and so there will be funding available," Dr Clark said.

"The way in which that fund is set up is a matter for policy advisors to best advise how we get the best value for money for those suffering from rare disorders is something that should concern us all."

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There are around 377,000 patients and families in New Zealand who live with a rare or life-threatening disease.

The organisation has been helping families for almost 20 years, after being set up to be a central starting point for families and people affected by rare disorders and linking them up with information and support groups.

Dr Bromhead acknowledged that the current system of funding under the Pharmac model meant the funds given out were based on the number of patients with a disease.

"And while, collectively, over 8 per cent of the population suffer from a rare disease, the number of patients for each disease is relatively small.

"Rare diseases just don't fit into this model and need to be evaluated differently. We need to start thinking about the value for the patient, not just the value for money.''

As well as this development, the organisation has also been told that its contract will be under review - something they are calling a "double blow".

"We are strongly advocating to the Government that NZORD's funding contract needs to continue so that [we] can provide vital services to patients.''

Dr Clark acknowledged the Government's move to invest $8 billion over four years into the country's health system.

For those struck with debilitating diseases, he hoped to ensure they had a better future.

"I don't want to risk setting up a fund that limits the number of people that gets access to medicines when it's possible that doing things a different way might help more people."