This paper identified the role of electronic payment system in promoting accountability in government ministries as well as the challenges facing the implementation of e-payment in government ministries in Ebonyi State. The study was guided by two research questions and two hypotheses. The population of the study comprised of 112 accountants as well as accounting education graduates working in the Ministry of Finance as accounting officers. The entire population was studied because of the small number of the population. A structured questionnaire was administered to all the respondents while 98 copies of the questionnaire were filled correctly and returned. The research questions were answered using mean and standard deviation while the hypotheses were tested using t- test. All the items except absence of a standard format for remittance of public funds were accepted as the challenges of implementing e-payment in government ministries in Ebonyi State.The test of hypothesis showed no significant difference on their responses based on gender and experience. The researchers based on their findings concluded that e-payment helps in assuring correctness of financial transactions recorded. The paper recommended that security of accounts details of e-payment beneficiaries should be prioritized to prevent hacking of such accounts; efforts should be geared towards the improvement of power as well as provision of alternative power; and Government should ensure adequate provision and maintenance of e-payment facilities.