Orakei chief executive Rangimarie Hunia today sent a written apology to Parsons and acknowledged the mistake.
"It has highlighted an error in our current processes and moving forward, we will be putting in place the correct technologies to enable the supply of a printed and digitised version of any individual's personal medical files, on request and at the clinic's cost," she wrote.
Documentation from the health centre to Parsons explains the fee was made up of "administrative costs" due to "resources like time, paper, ink". Parsons' file involved copies of 120 pages.
He believes the practice of charging patients for copies of their medical files was likely more common and widespread than people thought.
Under Ministry of Health's Health Information Privacy Code 1994, a private organisation can only fix a charge for making information available to someone when the request is for the same or substantially same information already disclosed in the previous 12 months.
The Code goes on to state that where a practice was charging they should complain to its manager in the first instance and if not satisfied complain to the commission.
The Medical Council of New Zealand stipulates the same rule, while The Royal New Zealand College of General Practitioners said it wasn't part of the complaints process.
A spokesman for the privacy commissioner said the centre's justification for the fee as an "administration" cost would have been assessed as part of its investigation.
However, he added private sector agencies - such as Orakei - could impose "a reasonable charge" which would depend on what type of information was provided, how much information - one box or 20 boxes - and how long it would take to prepare and delivery, ie, courier.
The privacy commissioner received a complaint of this nature about once a month, he said.
Private agencies couldn't charge for the time taken to review the information while making a decision as to whether to provide the information.
Parsons, 42, said he first made the request a few months ago as he had open heart surgery nearly six years ago.
Since then there had been significant stories in the media about Kiwi's getting into trouble while travelling overseas and he wanted a copy of his file on hand to give to his insurance company.
"I wanted to have a copy of them just to be on the safe side so if I go away on holiday or if I need them urgently I can store them all on my Dropbox.
"There's been a few stories recently about people with travel insurance and I always do ring up and declare and I have said to travel insurance is it easier if i give you a copy for your file, but if I ever have to go to hospital abroad then I've got my medical notes with me."
The software developer said although he was pleased the centre had decided to refund him his money, he felt like it wasn't a one-off situation and there would likely be unsuspecting Kiwis getting sucked into coughing up money they didn't have to, either at this health centre or other around the country.
"I'm thinking this is just the tip of the iceberg. I would say that I'm not the only person that they've charged this for."
He had nothing but praise for the doctors and nurses who worked at the centre but said he'd just experienced difficulties over administration issues.