A rock was used to smash the window but he did not believe other weapons were involved, Mr Hill said.
The station is open 24 hours but the doors are locked at night for security reasons. Customers pay through a small window near the till.
The staff member has been offered support, including counselling, he said.
"It's so unfair. This guy is just trying to make an honest living and this is just horrific. It's just not the Kiwi way."
A police spokeswoman said this afternoon three people had been arrested in relation to the incident and charges had been laid.
The crime squad were at the scene this morning as the investigation continued, she said.
Burger King Takanini shares a building with the station and the fast food outlet's manager Shivnesh Shankar told the Herald a large pane of glass had been smashed.
"The hole is big enough to climb through."
Mr Hill said incidents of people smashing their way into service stations was a "developing problem".
"Over the last three to four months there has been an escalating problem of people either using vehicles or other things to smash their way in ... and then groups of people taking cash and tobacco ... across Auckland."
A similar incident occurred at another Z station last week and he was aware of rival service stations also being affected, Mr Hill said.
"Our concern is it's only a matter of time before someone gets hurt."