BackgroundAssessment of the availability of essential medicines, in rural areas of countries with free state health care system, is scarce. Dependence on essential medicines among the population in rural sector is considered to be high. Assessing the availability of essential medicines in selected state owned primary and secondary health care institutions of a rural district will help to identify areas where improvement is needed.MethodsA descriptive cross sectional study, covering selected five primary and one secondary care institutions of a rural Sri Lankan district, was conducted. The national list of essential medicines, Sri Lanka was used as the check list and the guidelines of the WHO–Health Action International were adapted.ResultsThe secondary care institution recorded an overall availability of 71%, whereas the average overall availability of the primary care institutions was 56%. Central dispensaries recorded the lowest availability. Lack of availability of medicines needed for the management of chronic kidney disease, snake bite and poisoning was noted.ConclusionsAvailability of essential medicines in most of the primary and the secondary care institutions were fairly high. Deficiency in medicines needed for the management of emergencies was noted. A need based annual estimate of medicines based on an essential medicine list is suggested.Electronic supplementary materialThe online version of this article (doi:10.1186/s12913-016-1969-2) contains supplementary material, which is available to authorized users.