The Enquirer understands that Network Rail is currently withholding up to £9m from main joint venture contractor AmeyInabensa.
Subcontractors are now claiming not to have been paid by the contractor with some threatening to pull-off the job.
The £2.8bn Great Western mainline upgrade has been dogged by delays and rising costs.
The cost of electrifying the line between Cardiff and London has risen by £1.2bn and the job was originally due to be completed by the end of last year.
An AmeyInabensa statement said: “AmeyInabensa is continuing to try and resolve an issue around the certification of work to electrify a section of the Great Western Mainline.
“We remain in close discussions with both Network Rail and our supply chain to get this matter resolved as soon as possible.
“Work, however, is continuing and key milestones continue to be met, so we do not anticipate any disruption to train services in relation to this issue.”
One site source said: “Subcontractors are not getting paid and things are pretty grim on that job at the moment.”