The Enquirer understands that a raft of companies have been hit with disallowed costs.
The main current flashpoint is understood to be the supply chain of the ATC joint venture of Alstom, TSO and Costain.
Subcontractors claim that previously agreed accounts are now being refused.
The Enquirer revealed earlier this year that a costs row was brewing as Crossrail tried to claw back cash from its busted budget.
One project source said: “It’s disgraceful the way the supply chain is being treated.
“They have done all that has been asked of them over the past four years but now because Crossrail are recouping some monies off ATC they are just passing on the costs to the subcontractors.
“There is a very tense atmosphere on the project.”
It is understand that some suppliers are taking legal advice into what they consider is a breach of contract and are preparing themselves for a legal fight over disallowed costs being passed on to them.
Unite national officer for construction Jerry Swain said the union is keeping a close eye on the situation.