This study examine Accountability and Performance of Public Sector Organisation at Ondo State Ministries Finance and Health with the aim of assessing the Accountability and Performance of Public Sector Accounting Standards (IPSAS) in Public Sector. The study adopted cross-sectional survey design with selection of two (2) Ministries in the Ondo state. Survey Design collected data using 5-Point Likert-Scale questionnaire format which was administered on sample of 40 of Accountants, Internal Auditors and Staff at the two Ministries captured in the state (i.e. Finance, Budget & National Planning and Health) of which 38 were returned. The data was analyzed using descriptive statistic in line with bar chart. Three hypotheses formulated were tested using Chi-square (χ²) Statistical Technique Method via Statistical Package for Social Sciences (SPSS Version 20) at 0.05(5%) level of significance. Findings reveal that strong positive relationship occurred between accountability system and the performance of accounting system in the Public Sector in the ministry of finance and health with P-value (0.007<0.05) and also, weaknesses or strength that can occurred due to the lapses in the implementation of Accounting System in the area in Ondo States with P-value (0.051<0.05). Conclusively, the strength of accounting system is a boost to Ondo state by way of improvement in transparency and accountability. The study therefore recommends that as accountability is the hallmarks for good governance, if Nigeria is to be a member of the twenty most developed nations of the world by the year 2020, political office holders, citizens and all stakeholders in the Nigerian project should embrace integrity, transparency and accountability in the management of public funds.