St Johnstone say "changes were implemented immediately" after being included on a list of companies highlighted for failing to pay employees the minimum wage.
The Scottish Premiership club were among 15 Scottish companies and 139 in the UK to be "named and shamed" by Her Majesty's Revenue and Customs.
It investigated between 2016 and 2018.
The Perth club were found to owe more than £14,000 to 28 workers, 25 of whom were apprentice footballers.
The club paid the employees the money following what they described as a "very lengthy scrutiny" of their working practices by HMRC.
"Due to the absence of written evidence to support our position in relation to hours worked as opposed to the actual rate of pay, the club was unable to disprove HMRC's estimate of the average hours worked per week by these employees," St Johnstone said.
"The hours of work undertaken by our apprentices was fully reviewed and changes were implemented immediately following HMRC's outcome. The perceived failure to pay three other employees the national minimum wage related to voluntary deductions from pay by these employees.
"The club prides itself in treating our staff fairly and we are extremely disappointed to find ourselves in a position whereby we are criticised for failing to meet national minimum wage requirements."
All the named companies were served a notice of underpayment between September 2016 and July 2018.
They were ordered to pay back the wage arrears to workers at the current rate, as well as facing fines of up to 200% of money owed - capped at £10,000 per worker.