Unions raised concerns about the pay and conditions of some workers on an energy-from-waste plant being built at Wilton, saying they had discovered undercutting pay rates and exploitative employment practices.
The GMB, Unite and Ucatt unions said migrant workers were not being paid the national rates.
Unite officer Steve Cason said a “coach and horses” was being ridden through national agreements.
GMB official Michael Blench claimed that “little attention” was being paid to the welfare of migrant workers.
The project is being built by CNIM Clugston on behalf of SITA Sembcorp for the Merseyside Waste Disposal Authority.
SITA Sembcorp (SSUK) said 750 people were on the site, employed by more than 30 different sub-contractors, adding: “SSUK does not agree that workers employed on site are exploited, or being treated deplorably.”
CNIM Clugston had consistently said all workers were paid a rate equivalent to union agreements, said a statement.
“We do, however, acknowledge the allegations made by the trade unions as a result of meeting with some of the workforce and we have launched a full and proper investigation into these claims.”
The news comes as Europe struggles to form a coherent policy on the migrant crisis, with thousands of refugees from Syria and parts of war-torn North Africa continuing to flee to the continent in droves.