New York regulators are not the first to be baffled by the oxymoron of a vending machine full of fresh food. Health officials in Chicago, where Farmer’s Fridge opened six years ago, were also flummoxed at first by what, if any, permit should be required, said the company’s chief executive, Luke Saunders.

Eventually, he said, he was given a license to operate, along with a special sticker to display on every machine with Mayor Richard M. Daley’s name on it — even though Rahm Emanuel was mayor at the time. The company also has machines in Philadelphia, Milwaukee and Indianapolis, and started operating in New York and New Jersey in July.

It may seem surprising that Farmer’s Fridge has come under scrutiny. The company’s machines, which are mostly in corporate cafeterias and hospitals, have more food-safety features than many traditional vending machines. The internal temperature of each machine is taken every five minutes and uploaded to company servers. Should a refrigerator reach an unsafe temperature, it automatically stops dispensing food. The machines also track how long food has been inside, and will not release a product after its sell-by date.

Last week, according to Farmer’s Fridge, the health department ruled that its machines were food service establishments. The company was required to file an application and pay $280 — the same amount a restaurant would pay — for each machine.

And while the department has bent some of the rules — Farmer’s Fridge says it will not need to offer a restroom at every machine — the company has had to meet some of the standards for a restaurant.

For example, Farmer’s Fridge will provide the department information about where hand-washing sinks are available to its drivers who stock the machines. (In the case of one machine, in a public building lobby, Mr. Saunders said the solution may be the bathroom in a nearby bodega.) The company is also adding thermometers to its machines so inspectors can read temperatures without consulting company records.