Mr Valand said he was worried burglaries would become more common as the price of cigarettes increased.
"It's happening quite a lot around the country, especially up in Auckland it's quite bad, petrol stores and dairies, everybody is getting targeted for smokes," Mr Valand said.
The burglary comes after several snatch-and-grab thefts of tobacco in Masterton late last month, which police are still investigating.
Mrs Valand said the burglary had left her worried about working at the store at night.
"It's a bit scary when it's a quiet time."
The couple were unsure how much they had lost as they had not yet finished counting the remaining stock.
It was frustrating to have to clean up the mess and replacing stock would leave them out of pocket, Mrs Valand said.
"We have to spend more money on that and we can't get much more."
Senior Sergeant Mike Sutton said it was likely the cigarettes would be on-sold.
"I think based on the amount taken it's quite likely that [profit] was the motivation. Otherwise it would mean someone has got a life-long supply of cigarettes."
Anyone with information can contact Masterton police on 06 3700 378 or call Crimestoppers anonymously on 0800 555 111.
