The Enquirer understands that Transport for London and Crossrail are questioning bills from contractors.
One site source said: “The contractors are being told that they won’t get paid bills for overtime on some weekends and overnight work.
“They basically flooded the job with workers getting paid top dollar doing all hours when worries about the deadline started.
“Now those bills are being questioned on the client side over who authorised them which is causing all sorts of problems.
“The site workers have already been paid so they don’t care.
“This is a problem for the main contractors but no doubt it will get moved down the supply chain as usual.”
Last month the Government provided TfL with a £350m bridging loan to keep Crossrail on track after its opening was pushed back to Autumn 2019 as the project went £590m over budget.