Canberra health inspectors have used new food safety laws for the first time, forcing two popular cafes to display closure notices.

The heritage-listed Gus' Cafe in Civic and My Cafe at Manuka were shut down on Friday by the Health Protection Service because they were unclean and failed to keep some foods at the correct temperatures.

Prominent red signs have been displayed on the doors of the eateries, notifying would-be patrons of the closures.

It is the first time the signs have been put up since laws were passed in the Legislative Assembly last month, forcing eateries to display closure notices when they are issued with a prohibition order.

Previously eateries were not required to notify the public.

My Cafe manager Jessica Fryer says the closure notices are embarrassing.

"The sign says serious breaches of safety and we're talking about basic wear and tear. We felt like it was some minor stuff and we were quite happy to close down the kitchen voluntarily for most of the afternoon and fix it," she said.

"Now there's this really horrible, embarrassing sign saying 'we're closed and we're dangerous', and we're not."

Ms Fryer says the eatery was not given a chance to address the safety concerns, receiving the inspection report only two hours before being closed down.

She says the closure is unfair.

"To have it drawn to our attention that maybe we could do things a bit better to keep things fresher - great, thanks for the feedback," she said.

"But to be closed down because of rotten luck, that's a bit unfair."

But ACT acting chief health officer Doctor Paul Dugdale says the closure notices were necessary.

"It was a clear risk to the public," he said.

"The food inspectors most of the time they will offer some advice and there's no question of closure, but there's always little things that can be improved. It's only when there's a clear risk to the public's health that a closure is put into place."

He says the closure notices are justified.

"They're a transparency measure, they're informing the public about what's going on but not the public at large," he said.

"It's just informing the patrons that go to that premise and there's no intention to notify things broader than that."

The cafes will remain closed until the health issues are addressed.