The Enquirer understands around 300 workers employed via labour agencies have been affected on the Area North site in the West Midlands where Balfour Beatty VINCI (BBV) is the main contractor.
The problem has been ongoing for months with workers plagued by light pay packets.
One site source said: “This has been causing real distress across the job for a long time now.
“The system just doesn’t work and the lads are getting fed-up with not being paid correctly.”
HS2 chiefs are vowing to overhaul the system and ensure workers get the right money.
An HS2 spokesperson said: “Our contractor Balfour Beatty VINCI (BBV) is aware that administrative issues in capturing data on its ‘Time and Attendance’ system have resulted in payment delays to a small number of people employed through BBV’s labour suppliers, and would like to apologise for the inconvenience caused.
“Improved processes are being been put in place to ensure quicker and more accurate data capture and to give labour suppliers direct access to the system.
“BBV will monitor these improvements closely over the coming weeks to ensure labour agency workers are paid appropriately, in a timely manner.”