The Fair Work Ombudsman has instigated proceedings against a retailer for allegedly underpaying its workers more than $40,000.

According to the watchdog, Myst Oz Pty Ltd, which trades as The Grotto on Acland Street in St Kilda, allegedly underpaid 43 of its staff more than $40,000 between 2006 and 2008.

Rebecca Pearse, the company’s sole director, is also being prosecuted by the FWO for her involvement in the situation.

The discrepancy was discovered in 2008 after the FWO received complaints from workers.

The workers employed were split between casual and full time shop assistants, storage service workers and retail managers. The underpayments were in relation to the minimum hourly rate, annual leave entitlements and penalty rates for weekend, public holiday and overtime work.

The FWO reports that Myst Oz has recently back-paid all 43 staff who were affected but legal proceedings will still be undertaken due to the large number of employees involved and the delay in rectifying the matter.

The FWO is seeking penalties against the retailer and its director for committing several breaches of workplace relations laws.

The maximum penalty per breach is $33,000 for Myst Oz and $66,00 for Ms Pearse.