The Enquirer revealed last week that a pay row has hit the job with Network Rail withholding up to £9m from main joint venture contractor AmeyInabensa.
Workers have now been told that a wave of compulsory redundancies could see around 100 Amey staff let go by the end of March following an extensive voluntary redundancy programme.
The move has stunned workers who were hoping to be redeployed on other rail jobs in the region as the Great Western Mainline winds down.
A joint venture of KeolisAmey was awarded a £5bn contract last year to operate the Wales and Borders rail services.
One worker said: “We were told that there would be plenty of work on the Wales and Borders contract.
“I’ve been forced to apply for vacancies on that but nothing.”
Another added: “While hundreds of Amey staff have taken voluntary redundancy, my Welsh colleagues and I have remained loyal to Amey and the Great Western electrification and will remain to see the project until the very end.
“Being treated with such disregard is a bitter pill to swallow.
“As loyal Amey staff we feel we have already proven our worth to the company and come with the skills to undertake many aspects of rail infrastructure which would be of great asset to the future of transport of Wales, – yet we face redundancy on 31 March despite all the new work which is planned literally on our door steps.”
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 but will not be ready until March.
The government also decided last April to cancel electrification of the section between Cardiff and Swansea.
An Amey statement said: “Since it was announced that the electrification of the line between Cardiff and Swansea would not go ahead, there has clearly been reduced demand in the industry.
“As a result, we have been demobilising our team on the Great Western Electrification Program, trying to find deployment opportunities for people wherever possible, in rail contracts across the UK. We have remained in close contact with employees and unions throughout this process.
“While some employees have chosen to opt for voluntary redundancy, we have been consulting with employees and the unions about a small programme of compulsory redundancy.
“We appreciate the impact this will have on some employees and will continue to support everyone who is affected.