Details of people's prescriptions are being fed into an online repository from pharmacies across the country.
The Ministry of Health says information is encrypted and kept in a secure system only accessible by approved health professionals.
But it admits that people who aren't satisfied with those measures cannot opt out.
All New Zealand pharmacies are now connected to the ePrescription service, and nearly all general practices will be on board within months.
Pharmacy Guild chief executive Lee Hohaia said people would be unlikely to notice a change.
Pharmacists would still take their script and enter the information into their own dispensing system.
"There is a view that there will be some patient benefit ... things like subscription subsidy cards," Ms Hohaia said.
"People who could be eligible are not always getting their eligibility, because members of their family might have gone to different pharmacies to fill their prescriptions."
If GPs are signed up, they can use the broker system to check if their patient's script has been filled, or give additional instructions.
That kind of use will reduce the chance of medication harm through poor communication, the Ministry of Health says.
Graeme Osborne, its director of information, told a parliamentary health committee yesterday that 25 per cent of general practices were currently signed on. That would grow to nearly 100 per cent by the middle of this year.
Mr Osborne was unavailable for interview yesterday. A ministry spokesman said an encrypted copy of a prescription is held in the ePrescription broker for three months after its expiry.
"The broker and its encrypted information sits within the Connected Health network, a secure private network only accessible by certified health information users."
The ePrescription service is one of the initial phases of the 2010 National Health IT Plan to allow for more eHealth records and sharing of information between health professionals.
The programme aims to collect and store medical information, including medications data, in one complete electronic record.
That would benefit patients - cutting down the number of forms filled out, as a more superficial example - but could also save the Government money with improved information sharing.
Mr Osborne has previously said that the move to digital records was an improvement from paper records, where information could be accessed without any knowledge.
• Patient information entered into pharmacists' own prescribing systems now gets put into an online repository.
• Information is encrypted to guard against privacy breaches and deleted three months after a script's expiry date.
• If GPs sign up they can use the broker system to check if scripts are filled and give additional instructions direct to the chemist.
• That communication will save time and reduce the chance of medication harm, the Ministry of Health says.