Pharmac is reviewing its funding of child cancer medication despite it making up less than 1 per cent of its budget.
But chief executive Sarah Fitt told Morning Report that cost was starting to increase as new medicines came to the market and other patients had questioned the fairness of it.
Under the current system, any medicine for paediatric cancer was automatically funded without a Pharmac assessment.
Fitt said the agency cannot ignore the inconsistency despite it being a difficult discussion.
"It has been raised that this is inconsistent with how we manage medicines for other populations, older children with cancer, or other paediatric groups or adult patients with cancer," she said.
"[We] totally understand it's a difficult discussion and we are conscious of the impact and we want to reassure everybody that all medicines currently being used will continue to be funded."
As well as seeking feedback from patients, Fitt said expert clinicians would be asked for their opinions.
Pharmac wanted to know if the current rule had enabled the "dramatic increase in [child cancer] survival we've seen".
Despite the funding only taking up less than 1 per cent of Pharmac's annual budget of $1 billion, the issue could not be ignored.
"The key thing is that it is increasing," Fitt told Morning Report. New therapies were coming onto the market and that could see prices increase.
One question in the discussion document would centre on extending the rule to cover older children with cancer as well, she said.
"We need to ensure that we are being consistent to these patients."
The aim of the document was to help Pharmac "unpick" all the information it needed to make an assessment.