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WH Smith, Marks & Spencer and Argos are among a string of companies named for failing to pay the minimum wage.
More than 200 firms face penalties of nearly £7m and must reimburse workers for breaches dating back over a decade.
WH Smith, Marks & Spencer and Argos all said the breaches were unintentional and had been swiftly remedied.
It is unclear how much they paid in fines, but the government said penalties amounted to up to 200% of the arrears owed.
"Paying the legal minimum wage is non-negotiable and all businesses, whatever their size, should know better than to short-change hard-working staff," said Kevin Hollinrake, minister for enterprise, markets and small business.
The National Living Wage and Minimum Wage rose by 9.7% this April.
According to the business department, some 63,000 workers were left "out of pocket" because of the breaches, most of which occurred from 2017-2019.
WH Smith was the worst offender, having failed to pay more than £1m to over 17,600 workers.
The retailer said it had misinterpreted rules around uniforms, having asked staff to wear specific coloured trousers, skirts and shoes without reimbursing them for it.
"Following a review with HMRC in 2019, and in common with a number of retailers, it was brought to our attention that we had misinterpreted how the statutory wage regulations were applied to our uniform policy for staff working in our stores," a spokesman said.
"This was a genuine error and it was rectified immediately with all colleagues reimbursed in 2019."
Lloyds Pharmacy was the next worst offender, having failed to pay more than £903,000 to 7,916 workers.
The chain has been contacted for comment.
Your rights if an employer does not pay minimum wage
It's against the law for an employer to pay less than the National Minimum Wage or National Living Wage, says the conciliation service Acas.
They also must keep accurate pay records and make them available when requested.
If an employer has not been paying the correct minimum wage, they should resolve the problem as soon as possible. This is even if the employee or worker no longer works for them.
The employer and employee or worker may be able to resolve the situation by talking informally about it.
The employee or worker can also make a formal complaint to the employer; complain to HM Revenue and Customs (HMRC); or make a claim to an employment tribunal.
M&S said it had only been named by the government because of an "unintentional technical issue from over four years ago".
The government says it failed to pay £578,390.79 to 5,363 workers.
But an M&S spokeswoman said: "This happened simply because temporary colleagues were not paid within the strict time periods specified in the National Minimum Wage regulations and was remedied as soon as we became aware of the issue.
"Our minimum hourly pay has never been below the national minimum wage, it is currently above it and no colleagues were ever underpaid because of this."
Sainsbury's, which owns Argos, was told to repay £480,093.58 to 10,399 workers.
It said a payroll error identified in 2018 had affected some Argos store workers and drivers dating back as far as 2012, before Sainsbury's acquisition of Argos.
The retailer said it had launched an immediate investigation and "put this right at the time".
"Since then we have completed the integration of Argos onto Sainsbury's systems which will prevent this from happening again."