It is understood the employees, who are from India, were not employed by the consortium building the major infrastructure scheme, but had been hired through a a sub-contractor.
Economy Secretary Keith Brown said he has written to the Home Office seeking reassurances over measures in place to tackle the use of illegal foreign workers.
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"It's important that the construction industry can responsibly provide the correct resource to support the delivery of our pipeline of infrastructure projects," he said.
"Across our projects, contractors have assured us that they carry out all business and operations in such a manner as to fully comply with and meet all legislative requirements, including all relevant employment laws."
Steve Dillon, Regional Secretary of UCATT Scotland, said the incident was one example of workplace abuses on the site after the projects consortium decided not to replace the UCATT convenor in October.
"To restore confidence on the project the Scottish Parliament must tell the contractors to give unions full access to the site and to re-appoint a convenor to deal with problems as soon as they occur," he said.
The suspects are due to appear before Dunfermline Sheriff Court.
(LM/MH)
