They took cash and filled a backpack with about $200 worth of spirits and liqueurs, then fled on foot across the Domain towards the skate park or the high school.
A second shop assistant ran to the back of the shop and called the owner while a man parked outside called police after seeing the girls enter the store.
The threatened assistant remained calm throughout the robbery and complied with the girls' demands. He was uninjured.
Police were examining CCTV footage in the hope of identifying the girls, who were described only as Maori and in their teens.
Derbyshire urged anyone who saw anything suspicious around McDonald's and Super Liquor about 9pm on Friday - including two girls running across the Domain - to call him at the Kerikeri station on (09) 407 9211.
