Employees interviewed as part of the investigation also stated that they did not record their start and finish times, or the number of hours they worked each day.
It was determined by the Inspectorate that the employer had breached minimum employment standards by failing to meet its record-keeping obligations.
Gary Herbert, named as the second respondent, accepted that he was the person involved in these breaches.
Herbert was in charge of directing the hunting guides' daily duties and organising clients' accommodation at the lodge.
"The failure to keep complete wage and time records has resulted in an inability to show that minimum wage requirements had always been met by the employer and has also meant that the employer has been unable to demonstrate that it has complied with other minimum wage entitlement provisions," authority member Helen Doyle said in her determination.
It said 17 employees were affected by the failure to keep time and wage records and 19 by the lack of information on holiday and leave.
"There appeared a desire for simplicity in the application of a flat rate to employees, who worked varying duties and hours with benefits of accommodation and food along with the same lines shared by guests of the lodge," Doyle said.
It found the flat-rate payroll system was a result of "intentional actions" and as a result, the lack of records meant it was not possible to accurately assess if there were minimum-wage breaches and the extent it affected employees.
New Zealand Mountain Huting Limited was ordered to pay $55,000 and Herbert $27,500 to the Labour Inspector for payment to the Crown Account within 28 days.