The routine inspections carried out over the last year include a litany of failings, ranging from a curry house and other premises being over-run with mice, slime-covered equipment and a cafe with no hot running water.
Mice caused some of the most serious problems including the temporary closure of the cafe Hendersons at St John's and the Heirapolis takeaway.
Other well-known venues to fall foul of the inspectors included Lancers Brasserie in Stockbridge and Bar Napoli in the New Town.
Details of the inspections were released to the Evening News under the Freedom of Information Act. The council, however, used an exemption clause in the Act to block the release of the identities of the three worst offenders, arguing that doing so could prejudice potential prosecutions, with the venues still under investigation.
Fines totalling 1,000 were given to the Shezan Tandoori in Union Place after owner Abdul Latif Ghani admitted failing to implement a food safety system recommended by the council.
William Johnstone, owner of the W.D. Johnstone food store in East Trinity Street, was fined 300 for trying to sell out of date crab terrine and other items.
All the other premises which were found wanting have since been reinspected and found to be up to scratch.
Henderson's branch established last summer in the basement of St John's Church, in Lothian Road, was closed voluntarily on 18 March after inspectors found the building "full of mouse droppings".
Owner Peter Henderson said the family firm had done everything possible to deal with the problem in the historic building.
"The cellar cafe at St John's had an issue with mice in the past," he said.
"We have worked closely with Ecolab, the global leader in restaurant hygiene, to deal with the issue."
Lancers was criticised in September for its "very poor" standard of cleanliness and other problems including a fridge which was warmer than the safe temperature of 5C.
The restaurant has refurbished the kitchen over the last six months, although the owners stressed this work had been planned before the inspection.
Manager Hussein Bodrul said: "We have made the highest changes. We just reopened and everything is perfectly clean."
Pizzeria Bar Napoli scored the lowest possible grades for hygiene, structure and management last month despite owner Giorgio Crolla being fined 1,500 for hygiene breaches less than a year ago.
Inspectors who checked the Hanover Street pizzeria after the offences in August said conditions had improved. Yet when they visited again on 9 March they found evidence of rats.
The popular restaurant, which has been in the Crolla family for decades, has undergone a 200,000 refit and a follow-up inspection showed conditions were much improved.
Mr Crolla said: "The council are very happy and we are very happy with how the kitchen is run."
Another repeat offender was the Clifton Fish and Chicken Bar, in Clifton Terrace, which had to be temporarily closed down by inspectors in February last year to clean up its act.
A routine inspection in September found temperature records were not being kept at the takeaway.
Owner Carlo Corolla said: "It is all cleaned up now."
The city's environment leader Cllr Robert Aldridge said the council was determined to work with food outlets across the Capital to ensure customers were properly protected.
He said: "The council's environmental health staff rigorously enforce food safety regulations to ensure any food purchased in the city is safeguarded."