Two balaclava-clad men confronted the Warrnambool manager in his 50s after he arrived at 4.20am to prepare for the store's early-morning opening.

Detective Senior Constable Gary Greene, of the Warrnambool Criminal Investigation Unit, said the restaurant manager was confronted met at the front door by two balaclava clad offenders wielding knives.

''They forced him inside and he was forced to open up a safe. An undisclosed amount of money was stolen,'' Detective Senior Constable Greene said.

''The restaurant manager was then struck to the head before the two armed men fled the store on foot. Both offenders were both wearing balaclavas and hoodies.''

Detective Senior Constable Greene said the restaurant manager was taken by ambulance to hospital with swelling to his head and he was being held for observation.

''Police are examining CCTV footage and we expect to release an image later in the day,'' he said.

''We will be relying on public assistance and information to help identify the offenders,'' he said.

Warrnambool Hungry Jack's manager Adela Condon said the restaurant was closed yesterday morning.

She said the store manager had been held up, bashed over the head by two men and a district manager from Melbourne would decide when the store would re-opened.

''The manager was wacked over the head. I Think he'll be all right but it's a terrible thing,'' she said.

Read more in tomorrow's Standard.