Police were called to the Brockville Supermarket at 5.35am after reports a window had been smashed and a man could be seen inside.
A police dog team was at the scene.
A 26-year-old man was arrested and appeared in the Dunedin District Court yesterday morning on the charge of burglary.
He was released on bail to remain at Wakari Hospital for a mental health report to be completed.
The defendant's bail conditions barred him from going to the shop.
This week, large quantities of tobacco were stolen from both the Port Chalmers Four Square and BP Mornington.
A police spokeswoman said there was nothing to suggest yesterday's incident was related to the earlier burglaries.
