Introduction Hospital discharge data provide an important basis for determining priorities for injury prevention and monitoring trends in incidence. This study aims to illustrate the impact of a recent change in administrative practice on estimates of hospitalised injury incidence and to investigate the extent to which different case selection affects trends in injury incidence rates.

Methods New Zealand (NZ) hospital discharges (2000–2014) with a primary diagnosis of injury were identified. Additional case selection criteria included first admissions only, and for serious injury, a high threat-to-life estimate. Comparisons were made, over time and by District Health Board, between hospitalised injury incidence estimates that included, or not, short-stay emergency department (SSED) discharges.

Results Of the 1 229 772 injury hospital discharges, 365 114 were SSED; 16% of the annual total in 2000, 38% in 2014. Identification of readmissions prior to the exclusion of SSED discharges resulted in 30 724 cases being erroneously removed. Age-standardised rates of hospitalised injury over the 15-year period increased by, on average, 2.7% per year when SSED discharges were included; there was minimal secular change (−0.2%) when SSEDs were excluded. For serious hospitalised injury, the annual increase was 2.3% when SSED was included compared with 1.1% when SSEDs were excluded.

Conclusion Spurious trends in hospitalised injury incidence can result when administrative practices are not appropriately accounted for. Exclusion of SSED discharges before the identification of readmissions and the use of a severity threshold are recommended to minimise the reporting bias in NZ hospitalised injury incidence estimates.