Merseyside Police said they were called around 6am after reports two men had ordered two members of staff on duty at the time to empty the safe after forcing them to the back of the premises.
A spokeswoman said the men escaped with "a significant quantity of cash inside".
Neither of the workers were injured but both have been left distressed by their ordeal, police said.
Officers are examining CCTV from the petrol station and surrounding areas and enquiries are on-going in surrounding areas.
Detectives are appealing for anyone who has any information about the incident to contact 0151 777 4065 or 101 or Crimestoppers anonymously on 0800 555111.