As a consequence of the lack of records E Ming had underpaid its employees a total of $23,878.89, and E Lynn had underpaid its employees a total of $30,746.61.
Labour Inspectorate retail lead Loua Ward said it was disappointing to see companies operating under established brands failing to provide staff with their minimum rights.
"These businesses have highly systematic approaches to the production of their product. It's quite unacceptable that they do not have a similarly systematic approach throughout their operations, to ensure compliance with minimum employment rights, for what can be very vulnerable workers," Ward said.
"It's simply not acceptable for businesses to 'fix things up' after the event. Businesses and their brands must have mechanisms in place to monitor and prevent employment standards breaches. It's the 'getting it right' that counts."
Ward said this case served as a warning to consumers: "Be mindful about whether your money is going into the right pocket. For a five dollar pizza, workers shouldn't have to pay the price."
Domino's said it had conducted a thorough wage audit following a staff complaint.
"Domino's expects all of its franchisees to comply with their New Zealand employment law obligations," a spokewomen said.
"As a result, the franchisee was removed from the business and any underpayments of team members found were immediately rectified."
In its determination, the authority said it must impose a penalty as a deterrent to E Ming, E Lynn and others who may not be minded to meet their obligations.
"The Authority must impose a penalty at a level that signals its disapproval of the conduct of E Ming and E Lynn in not meeting minimum standards obligations and which acts as a deterrent to E Ming, E Lynn and other employers who may not be minded to meet their obligations," the authority said.
Both franchises were taken over by Domino's Pizza Enterprises on 28 February 2017 which subsequently purchased them.
Xi (Bruce) Chen is a director and shareholder of both E Ming and E Lynn.