The Cloughmills company was £3.2m in debt in 2005
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Employment Minister Sir Reg Empey has asked police to investigate employment and workplace practices at Reid Transport.
The firm went into administration on Wednesday, with the loss of 200 jobs.
Sir Reg said he had called in the police after allegations were made by members of staff.
Employees are continuing to hold a protest outside the company gates in Cloughmills, County Antrim, over unpaid salaries
The trade union Unite has called on the Northern Ireland Executive to make emergency payments to the workers.
Union representative Sean Smith said that many workers have been told they will not be compensated.
"I met minister Empey yesterday (Friday) afternoon we had a very frank and open talk and he admitted that not all people will be getting redundancy," he said.
"The under 18s will not be getting redundancy, less than two years service will not be getting redundancy and the foreign nationals who have no national insurance number will not be getting redundancy."
Sinn Fein assembly member Daithi McKay said there was anger that the minister could not guarantee earlier assurances that 200 workers would receive redundancy payments.
On Friday it emerged, according to Reid Transport Ltd's latest accounts, it was £3.2m in debt in 2005.
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