Victims say Edinburgh Trams has blamed Scottish Water, which in turn has blamed the tram scheme's organisers for the incident six months ago.
It is unclear how many buildings were affected as owners are claiming there have been further problems since at least three properties were flooded in May.
Firms in the capital's West Maitland Street and Grosvenor Street area, who have been given sandbags to combat a repeat of the problem, are calling in their own surveyors to examine the sewage system they claim is still not fully fixed.
Insurers are struggling to claw back cash as the investigation by Scottish Water and Edinburgh Trams into who should bear the responsibility for the flooding continues.
One firm claims it has cost it at least £250,000 while another, Macphersons the Kiltmakers, plans to pursue compensation for seepage.
Alison Adamson-Ross, who runs the family business, said not enough has been done to make the underground pipes safe.
She said: "It doesn't feel safe and I'm going to have to get it surveyed myself because I don't trust them.
"We also have a very strong smell in our basement, and damp. We have never had damp before. I have a store full of tartan and if it happens again I don't know what we'll do.
"I feel we are living on a time-bomb and we've already used up all our rainy-day money and can't afford to move."
The firm claims the initial flood penetrated its basements and wants surveyors to check on this damage as well as the pipes.
Another trader seeking compensation, Muhammed Hussain, said his Omar Khayyam restaurant was closed for five months after the flood.
He said: "We've not been able to get any answers all this time. The trams blame Scottish Water and Scottish Water blame the trams."
The Herald revealed earlier this month that the taxpayer faces a bill of more than £10 million to compensate shops and other firms for lost business by the end of the year, with warnings the total will go on rising.
Claims for money lost because of the controversial project are being lodged at the rate of more than 10 per month.
Edinburgh Trams and Scottish Water said they could not comment on the issue until the investigation was finished.
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