To determine the prevalence of medication administration errors and identify factors associated with medication administration errors among neonates in the neonatal intensive care units. Prospective direct observational study. The study was conducted in the neonatal intensive care units of five public hospitals in Malaysia from April 2022 to March 2023. The preparation and administration of medications were observed using a standardized data collection form followed by chart review. After data collection, error identification was independently performed by two clinical pharmacists. Multivariable logistic regression was used to identify factors associated with medication administration errors. A total of 743 out of 1093 observed doses had at least one error, affecting 92.4% (157/170) neonates. The rate of medication administration errors was 68.0%. The top three most frequently occurring types of medication administration errors were wrong rate of administration (21.2%), wrong drug preparation (17.9%) and wrong dose (17.0%). Factors significantly associated with medication administration errors were medications administered intravenously, unavailability of a protocol, the number of prescribed medications, nursing experience, non-ventilated neonates and gestational age in weeks. Medication administration errors among neonates in the neonatal intensive care units are still common. The intravenous route of administration, absence of a protocol, younger gestational age, non-ventilated neonates, higher number of medications prescribed and increased years of nursing experience were significantly associated with medication administration errors. The findings of this study will enable the implementation of effective and sustainable interventions to target the factors identified in reducing medication administration errors among neonates in the neonatal intensive care unit. We adhered to the STROBE checklist. An expert panel consisting of healthcare professionals was involved in the identification of independent variables.