Mr Smith said the staff member had followed all correct procedures and had notified the police, who were on-site "very quickly".
He said the staff member, who had a young family, was "quite upset", as were the rest of his employees following the incident.
"Their work place has been invaded. They feel their work place has been violated for a high-risk crime with little reward." Mr Smith said the station had seen "smash and grab" burglaries in the past but this occasion had been the first time it had been robbed during trading hours.
"It does get you a bit upset when these things happen but there's not much you can do about it.
"You just have to move on and help the police as much as you can."
Police say they are looking a Maori or Polynesian male, tall, and of solid build.
He was wearing a black hooded sweatshirt, grey track pants, and a bandana across his face.
Police have been examining the scene and talking to people in and around the area.
"This person has targeted the lone shop attendant, brandishing a weapon and demanded money be handed over," said Detective Sergeant Mike Smith.
"Obviously this has been a terrifying experience for the staff member and police are working with Victim Support to provide support to this victim".
The crime was captured on CCTV and police are asking anyone with information that can assist in identifying this person to please contact the Masterton Police on 370 0300.
Alternatively, you can provide information anonymously on the CrimeStoppers line 0800 555 111.
Mobil re-opened its doors for trading at 1pm yesterday.