McColl’s has been accused of stripping away “a crucial level of support” by paying staff below the minimum wage.
The convenience store chain was the second-worst offender on the government’s list of 117 employers who underpaid workers.
It owed a collective £258,047 to over 4300 employees.
McColl’s, which made a gross profit of £301 million last year, blamed its processes for recording staff attendance.
It claimed to have reimbursed and apologised to “affected colleagues”.
Tesco-owned One Stop Stores came just below McColl’s on the list, being forced to hand over £56,505 in back-payments.
In total, the “named and shamed” companies must pay £2.1 million to over 34,000 employees, plus a £3.2 million fine.
John Lewis committed the biggest breach of employment law, withholding £941,355 from almost 20,000 staff.
The retailer, which is the UK’s largest employee-owned business, pointed the finger at a “technical breach” in its “pay averaging” system.
“Our minimum wage laws are there to ensure a fair day’s work gets a fair day’s pay – it is unacceptable for any company to come up short,” small business minister Paul Scully said.
“All employers, including those on this list, need to pay workers properly.”
However, Trades Union Congress economics head Kate Bell suggested the list is “likely to be just the tip of an underpayment iceberg”.
“Minimum wage workers have been at the heart of the pandemic, and deserve a decent wage of at least £10 an hour,” she told the BBC.
“But these figures show many workers aren’t even being paid the legal minimum, with household name employers flouting their responsibility to properly pay staff.
“Government should step up inspections to catch every employer that underpays staff.”
Pret A Manger, Welcome Break and The Body Shop were also named on HMRC’s list.