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The man entered the dairy on Eglinton Rd around 8am and demanded money and cigarettes from staff.
The man then ran from the store, police said.
Two assistants in the shop were shaken but unhurt in the incident.
Early inquiries suggested the man may have been in the area for up to an hour before the robbery, Detective Sergeant Rob Hanna, of Dunedin, said.
He is believed to be Caucasian, in his 20s, 175-185cm in height and of slim, athletic build.
He was wearing a distinctive multicoloured hoodie with a white background and coloured design, and three-quarter trousers and boots. He was carrying a number of bags.
''Police would like to hear from anyone that was approached or spoken to by a male fitting the alleged offender's description. Police would also be interested in hearing from anyone who has been offered cigarettes or tobacco since the robbery,'' Det Sgt Hanna said.
Anyone with information should call Dunedin Police on 03 471 4800 or information can also be provided anonymously via Crimestoppers on 0800 555111.