The National Standards of Education (NSE) plays an important role in controlling the quality of education because it contains some aspects for the educational system. The purpose of this research is to strengthen the implementation of the education quality assurance system. This study used a combination of a quantitative and qualitative approach. Data was 33.664 for quality report assessment at elementary schools in academic year 2016/2017 combined with the result of questionnaire and Focus Group Discussion (FGD) with teachers, the school principal, and school supervisors in Yogyakarta City and Tarakan City. The results of statistical analysis indicate only process standard, graduate competency standard, financing standard, and assessment standard that have already achieved the level of NSE 4. The lowest value achieved is the educator standards (3.18), which means that the qualifications of educators are still relatively low. Research also found out that the Internal Quality Assurance System (IQAS) gives a benefit to improve the learning quality while FGD shows that almost all standards affect the graduate competency standard.