Sergeant Blair Wilkinson, of Oamaru, said police were investigating whether the burglaries, at 5.30am and 4.20am, were linked.
Cigarette robberies have been increasing - there were a series of them in Dunedin in January at service stations.
Palmerston Four Square owner David Muir said he was ``pretty disappointed'' by the burglary, and it has made him rethink the security measures he had in place. No-one was in the shop.
Senior Constable Stefan Witehira, of Palmerston, said security camera footage was being reviewed.
Maheno Service Centre operator Garrie Ford said robberies went ``with the territory'' for garage owners.
He was disheartened by what occurred.
``You've just got to take it on the chin. We've been burgled before and we'll be burgled again.''
Mobil Eastgate owner Robyn O'Callaghan, robbed on January 24, said at the time ongoing thefts of cigarettes made her question stocking tobacco products. But she was hamstrung, as the stations needed to sell them to compete with rival outlets.
This incident was preceded by two ram-raids on BP services stations in Dunedin.
The cost of cigarettes has leapt in recent years. The fourth consecutive yearly 10% tax hike on tobacco products was imposed from January 1 this year. The average cost of a packet of 20 is about $23.
Mr Muir said he did not know if the price of cigarettes was a factor in the burglary of the Palmerston shop he had run for two years.
During that time this was his only burglary.
``We know it's happening a lot up north, but we didn't think it would happen down here.''
He said all necessary security precautions had been taken, but the offenders still got in.
``I'm just really happy it didn't happen during working hours and very happy none of our staff were around or injured. You can replace cigarettes, not people.''
