This research aimed to test the contribution of internal control system and accountant competence to the quality of financial report that implemented government accounting standard as intervening variable at Puskesmas. The data collection in this research was collected through survey. Questionnaires were distributed to the Head of Administration Division and Financial Staff or Accountants of puskesmas in Yogyakarta Province. The sampling technique was cluster sampling to determine the population area and convenience sampling to determine the samples of puskesmas. The research result showed that there was a positive and significant relation between the internal control system and the implementation of government accounting standard to the quality of puskesmas financial report; and there was positive but insignificant report between accountant competence to the quality of puskesmas financial report. There was positive but insignificant relation between internal control and positive and significant relation between accountant competence to the implementation of government accounting standard. The internal control system gave positive but insignificant relation; and accountant competence gave positive and significant relation to the financial report quality of puskesmas through the implementation of government accounting standard.