A series of inquiry laptops were stolen in the raid at its Waverley Gate headquarters but it is understood no other firms within the complex were targeted.
Sources within the building could not rule out the possibility that the inquiry had been deliberately targeted by crooks aiming to disrupt the gathering of evidence or access to confidential information.
Councillor Joanna Mowat, Tory transport spokeswoman, said there were concerns the heist has been carried out to conceal information.
She said: “It’s very worrying that some people might be so concerned about what might come out that they would go to the length of breaking in to steal laptops.
“We have to make certain that this wasn’t an opportunist attack, but if this does prove to be a targeted attack, that is extremely concerning.
“The sooner that the inquiry gets under way and starts reporting its findings, the better, because if people have gone to those lengths, you can only assume they were quite keen to cover something up.”
The break-in has raised fears that sensitive information that could jeopardise the anonymity of whistleblowers may have been seized.
“If there were whistleblowers who had provided information [to the inquiry], you would have to assume they would be very concerned,” Cllr Mowat added.
The raid took place between Thursday evening and Friday morning at Waverley Gate in Waterloo Place – a district right in the heart of the city centre. No other business occupying the building was broken into.
Tram inquiry offices lie on the first floor of the building which is only accessible via a staircase or elevator in the lobby. A key card is essential to gain access to the building.
The inquiry team declined to reveal how many laptops were stolen and whether intruders had forced their way in.
In November, the hearing became a full-scale public inquiry – giving the chairman Lord Hardie powers to compel witnesses to appear – after complaints that witnesses had failed to co-operate.
Councillors will next week be asked to approve a confidentiality waiver for council staff allowing them to provide information to the inquiry without fear of breaching their contracts.
A spokesman for the council said: “We will be seeking assurances from Lord Hardie’s office that no council data provided to the inquiry team has been compromised as a result of the break-in.”
A solicitor told the News that if the inquiry failed to protect information sufficiently it could face a fine of up to £500,000 for breaching data protection laws.
An Edinburgh Tram Inquiry spokesman said: “As the incident is currently under investigation it is not appropriate to comment further.
“We can confirm that the stolen equipment incorporated the highest levels of encryption in line with Scottish Government security policy.
“Work will continue at the Edinburgh Tram Inquiry in accordance with the published order of events.”
A spokeswoman for Police Scotland said: “Officers are investigating following the theft of computer equipment from a city centre office in Edinburgh sometime overnight between Thursday, January 29 and Friday, January 30.
“Inquiries are ongoing. Anyone with information should contact Police Scotland on 101 or call Crimestoppers anonymously on 0800 555 111.”