This article presents results from the consideration of epistemic uncertainties in New Zealand (NZ) probabilistic seismic‐hazard analysis. Uncertainties in ground‐motion prediction are accounted for via multiple ground‐motion prediction equations within the logic‐tree framework. Uncertainties in the fault‐based seismicity of the earthquake rupture forecast due to uncertainties in fault geometry, slip parameters, and magnitude‐scaling relationships are considered in a Monte Carlo simulation framework. Because of the present lack of fault‐specific data quantifying uncertainties for many faults in NZ, representative values based on judgement and available data for NZ and foreign faults were utilized. Uncertainties in the modelling of background seismicity were not considered. The implications of the considered epistemic uncertainties in terms of earthquake magnitude–frequency distributions and probabilistic seismic‐hazard analyses for two spectral acceleration ordinates, two soil classes, and two locations (Wellington and Christchurch) are examined. The results illustrate that, for the uncertainties considered, the variation in seismic hazard due to the adopted ground‐motion prediction model is larger than that due to the uncertainties in the earthquake rupture forecast. Of the earthquake rupture forecast uncertainties considered, the magnitude‐geometry scaling relationships was the most significant, followed by fault rupture length. Hence, the obtained results provide useful guidance on which modelling issues are the most critical in the reliability of seismic‐hazard analyses for locations in NZ.