£1.44m in back pay has been identified for 22,400 workers across all those companies, with reasons such as deducting the cost of uniforms or failing to pay for travel time.
Two Christian companies were on the list. Methodist Guild Holidays Limited, trading as Christian Guild, are a multi-denominational Christian holiday organisation and were listed as having failed to pay £29,255.09 to 136 workers, with average arrears of £215.11 per worker.
The second was The Christian Conference Trust, who provide buildings for events such as church weekends away and charity talks. They were listed as having failed to pay £15,479.62 to 28 workers, with average arrears of £552.84 per worker.
Premier contacted both to understand what caused them to be on the list and both responded.
John Moffoot MBE, the Chair of the Christian Guild, said: "The first things to say is that none of the Christian Guild staff who were on the national minimum wage were ever underpaid their annual salary. What the national minimum wage audit has shown is that where that happens - and staff elected to be paid monthly - in those months where there are 31 days in a month they are technically being underpaid even though they've got a twelfth of their salary. It's a very technical thing.
"We've reimbursed all the staff who were affected by the technical underpayment, we've revised our pay processes so it doesn't happen again."
When asked if the staff were caused distress Moffoot replied: "None of them knew about it until the national minimum wage auditors paid attention to it so they're not going to object to getting a few years of back pay. And the back pay ranged from just a few pounds to a few hundred pounds in some cases, but I don't think they're going to object to that."
He added: "We were upset that we were picked out in this way. I suspect we are not alone in this, I suspect more and more employers are going to be found to have done exactly the same thing with any monthly paid staff.
"We've amended our pay processes so it doesn't happen again."
The Christian Conference Trust told Premier the error was inadvertent non-compliance and that employees had not suffered any loss of pay but had not been paid in the timing required by the National Living Wage rules.
They said in a statement: "Obviously this is very disappointing for the charity because the payments to affected employees relate to technical underpayments rather than actual underpayments."
The Christian Conference Trust had used a system of spreading employees' pay across the year, with the consent of staff, meaning pay had then not technically complied in a certain month if an employee had worked more than usual.
They said: "We believe that we have now identified all the occurrences of this anomaly in the past, and have made additional payments to the small number of current and ex-employees affected.
"Further, we have worked with HMRC to ensure that our pay arrangements and practices are fully compliant with the way that the NMW legislation works, in order that this situation does not re-occur in the future."
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