Police were called to the Normanby Tavern, in Northeast Valley, just after 8pm, following reports of a robbery.
Senior Sergeant Steve Aitken said the publican was locking up the rear of the pub when he was grabbed in the dark car park behind the building.
"He was grabbed from behind and a sharp instrument was held to his chin and neck area."
The offender then demanded cash, and the publican handed over a "sum of money".
The offender was seen running down Antrim St towards North Rd, Snr Sgt Aitken said.
He was described as about 177cm tall and wearing dark clothing.
The publican, who received a small nick to his chin from the sharp object, was left "very shaken" by the ordeal, but did not require medical attention.
"There is an air of premeditation about this. It appears the offender has been waiting for the man to come out, and it would also appear he has some knowledge of the procedure for shutting up the pub."
Police put a cordon in place, and a dog team tracked a short distance down North Rd before losing the scent.
A scene examination was expected to continue this morning.
It was too early to say if the incident was linked to the armed robbery of Forbury Pharmacy by a knife-wielding man on Wednesday, he said. The man made off with a quantity of prescription drugs.
Anyone with information was urged to contact Dunedin police on (03) 471-4800 or Crimestoppers on 0800-555-111.
