Thornton added that the scheme's business case is marginal, even without the listing complication.
A report by the SRA is understood to mirror this view.
Although the extension would not run through the viaduct, it would run adjacent to it. If the viaduct was listed, it would become more difficult to take down surrounding structures.
English Heritage wants the entire goods yard to be listed, which would be the end of the project, according to Thornton. But it is thought that culture secretary Tessa Jowell is unlikely to list the entire 4.2 ha site.
A decision on the listing has been delayed and is not expected for another two weeks. It is understood that the Department for Culture, Media and Sport is investigating whether the viaduct really was designed by John Braithwaite, as records suggest, and what effect it would have on the listing if he was not the engineer.
A further twist has been the launch of a second judicial review by goods yard tenant Will Bailey. Among Bailey's claims are that there is no reliable assurance that the extension will go ahead and that LU's listed building consents for the site have expired.
Previously Bailey launched a judicial review against Hackney Council, which still continues.