A prohibition notice was issued by ACT health authorities forcing the Bread Nerd premises at Hume to close and clean up early yesterday.
By 4.30pm, the breadmakers had cleaned the site to the satisfaction of inspectors, and were able to reopen their doors.
Chief Health Officer Paul Kelly said inspectors visited the site on Wednesday after a complaint about a food product, which contained a contaminant.
On their Wednesday visit to the bakery, also known as That Bagel Place, inspectors spotted problems that were a significant threat to public health.
Dr Kelly wouldn't give details but said there were concerns about cleanliness.
Inspectors took 140 photographs of places of concern.
Dr Kelly welcomed the outcome of yesterday's action. The proprietors had cleaned up in record time and were able to re-open before the end of the day.
''They needed reminding that they needed to raise standards of cleanliness and they've done that,'' he said.
''Our inspectors have been out again and they're satisfied that what's there is fine.''
No decisions have been made about whether to prosecute.
Sharon Peart, who owns Bread Nerds with baker husband Shane Peart, said they had been told nothing of a contaminant in a product.
Rather, they had been told a customer had reported seeing mould in a bread basket - which wasn't in fact mould, but flour.
Inspectors had raised concerns about flour stuck to the floor, especially in wet areas.
Mrs Peart said they had put a cleaning management plan in place, as requested, and were now cleaning every day, rather than on Mondays, as requested.
They would also have staff trained, as requested.
''We're disappointed, and last night we were stressing out, but really when you look at it, you've got to get in there and do what they want, not get annoyed … We listened to what they said and got in there and fixed it.''
They lost a day's trade, and were to start work at midnight last night.
Bread Nerds began as That Bagel Place in Isaacs, and now operates from a large space at Hume, where the business makes bagels, pastries, pies and well-regarded sourdough bread.
It has become one of the largest private bakeries in the city, supplying about 20 outlets, including some IGA supermarkets, and selling also at the markets. Health authorities have powers that can range from a verbal warning to prosecution.
Dr Kelly reiterated his position that prohibition notices were not issued lightly, only when there were grave concerns about public safety. Forty-two prohibition notices were issued in the year to the end of June. None were issued in July.