The company building the HS2 rail line between London and Birmingham has reported one of its subcontractors to the tax authorities over possible fraud.

Whistleblowers made allegations over the way pay was handled for some construction staff on the high-speed line.

HS2 Ltd said last month it was conducting its own investigation, looking into two firms who supplied it with workers. The company has now also referred the matter to HMRC.

The firms in question were providing workers to Balfour Beatty Vinci (BBV), a contractor for HS2.

Transport Secretary Heidi Alexander is expected to raise the issue in Parliament this week. It is the latest difficulty to beset the troubled giant rail infrastructure project.

HS2 has faced myriad challenges and spiralling costs since it was first announced in 2009.

It was originally designed to boost capacity on the railways between the north and south of England but the last, Conservative, government decided to scrap the second phase of the project, which included building lines to Manchester and Leeds.

Earlier this year whistleblowers flagged concerns over the way some subcontracted staff were being paid. They said self-employed workers had been falsely declared as salaried staff, with “fake” payslips submitted at a higher payrate. The allegations were first published in the i newspaper in May.

One of the labour suppliers is understood to remain suspended from new contracts while inquiries continue.

An HS2 spokesperson said: “We treat all whistleblower allegations seriously and are continuing to conduct our own investigation.”

The firm said it encouraged anyone with relevant information to report it via confidential internal channels.

The Department for Transport said last month it had “a zero-tolerance attitude towards fraud, bribery, and corruption” and would ensure any claims of wrongdoing were thoroughly investigated.