"He's heard all the noise and called the police," he said.
Police CIB staff would be back at the scene this morning.
Raffan said it was too early to say if it was linked to a series of other aggravated robberies that have plagued the district in recent weeks.
It's the second armed incident to occur at BP Horotiu this year after it was targeted in March by three men armed with screwdrivers.
Michael Hill in the Centre Place Shopping Centre, McDonald's Greenwood St and two dairies have been hit armed robbers in Hamilton between July 8 and July 12.
Raffan said this morning's incident was classified as burglary as the staff member was not threatened by the thieves.
Anyone with information is asked to call Hamilton police on 07 858 6200.