Caversham Pharmacy owner Stephanie Corby said the break-in, which happened yesterday morning, left her feeling "pretty gutted".
She started dealing with the aftermath of the break-in about 5am, shortly after the incident happened.
It was the second such incident since she bought the business in April and she was now looking at options to upgrade the shop’s security system.
She did not believe the previous owner, who had owned the business for about 17 years, had experienced similar incidents.
Nearly all of the prescriptions which had been packaged up to be collected had been taken in the break-in, Ms Corby said.
Thieves failed to get into the securely locked dispensary area where controlled drugs were kept in a safe.
Ms Corby’s message for the offender was to "think about who you are doing this to", as her shop was a small local pharmacy, owned by a person with a young family to support.
Constable Nick Turner, of Dunedin, said an Armourguard commercial alarm activation was sounded at the pharmacy about 4.40am.
