Since 1995, air transport operators in New Zealand have been able to meet the flight and duty time (FDT) regulations by operating according to prescriptive FDT limits or by seeking approval to operate under a potentially more flexible company‐specific FDT scheme. There has been no formal assessment of the impact of this increased flexibility on fatigue management processes. The aim of the present study was to determine the strategies and processes that commercial aircraft operators in New Zealand have in place for managing fatigue and whether these differed according to the type of FDT system under which organizations were operating. All air transport operators in New Zealand were sent questionnaires that were to be completed by an individual in a management role, a line pilot, and an individual in a rostering role. Questions were asked about the FDT system under which the organization operated, the strategies and processes in place for managing fatigue, and the consequences of the organization's approach to managing fatigue. One hundred and fifty‐three responses were received from 88 organizations (55% of all air operators) and were representative of the structure of the New Zealand industry. Air operators were most likely to report that they monitored flight and duty times and pilot workload to manage fatigue (used by 90–99% and 70–90%, respectively), while educating rostering staff and reviewing the processes for managing fatigue were the least utilized strategies (used by 36–50% and 39–60%, respectively). Within the same organization, managers were more likely than line pilots to report the use of specific fatigue management strategies. There were no differences found between organizations operating under prescriptive regulations and those using a company‐specific scheme on ratings of how well fatigue was managed, the number of fatigue management strategies employed, or the frequency of use of selected strategies. Across the industry as a whole, the provision of more flexible regulatory options has not greatly changed fatigue management practices, although some operators have implemented innovative strategies. The findings suggest a need to raise the level of knowledge within the industry regarding the causes and consequences of fatigue and of processes for its management. This is further supported by the discrepancies between the responses of line pilots and managers, which raise doubts about the effectiveness of some strategies nominally being employed. The regulator and other relevant industry groups should consider how to move the industry toward a mature safety culture and solid knowledge base because these are fundamental to more flexible fatigue management regimes, as is adequate regulatory knowledge, support, and oversight.