Experts have warned that the New Austrian Tunnelling Method (NATM) would threaten the structural stability of the capital's iconic towers.
The proposed technique has already been linked to high-profile disasters such as the 1994 Heathrow Express cave-in and the Barcelona Metro collapse less than two months ago.
Sources in the Corporation of London are particularly concerned about the use of NATM, in which tunnel walls are lined with sprayed concrete, in the construction of the proposed Barbican crossover.
Running beneath the Grade II-listed complex, this 150m-long section of the cross-city rail link could end up being as big as the 'Swiss Re building on its side'.
According to a detailed report by Alan Baxter & Associates, the potential impact on one of the Barbican's key buildings, Defoe House, 'is particularly significant'.
The survey claims that unless 'appropriate protective measures' are introduced, the damage caused by possible land movements during the construction of the tunnels, stations and shafts could be 'severe to very severe'.
Barbican residents have written to the Corporation of London urging its planning and transportation committee to carry out a 'condition survey' of the complex before work begins, amid fears that the tunnelling could affect the 'structural integrity of the estate'.
Meanwhile, among the other 320 listed buildings that may be at risk from land settlement, are some on Charterhouse Street, Cowcross Street and those at the eastern end of Smithfield Market.
The proposed excavations for the Lindsey Street ticket hall could also have an impact on the neighbouring Grade II*-listed market buildings.
Joe Weiss, the Corporation's strategic transportation director, stressed there were a number of serious challenges ahead for the Crossrail scheme.
He said: 'Its construction, particularly under sensitive sites, including the Barbican, will require robust and proven technology to satisfy the Corporation and its residents.
'There are no problems, just issues, all of which can be resolved. We are extremely keen to work with Crossrail and with their expertise we can come to an early resolution,' he added.
Crossrail was unavailable for comment as the AJ went to press.