The alarming incident happened at the Tesco Express store on Poolstock Lane on Wednesday morning.
Other news: Dismay at Wigan community group after callous thieves break into its headquarters and steal donated itemsGreater Manchester Police (GMP) said two men, one armed with what appeared to be a firearm, made threats and then left the scene with a quantity of cash.
Enquiries are ongoing.
A post on social media from a shocked shopper said two men were wearing balaclavas and described the weapon as a sawn-off shotgun.
The post also said residents in the store had been barricaded inside during the dramatic incident.
A large police presence was seen outside the store on Wednesday morning, with the building taped off.
A Tesco spokesperson said: “This was a distressing incident for our colleagues and we are supporting the police with their investigation.”