This research was carried out to analyze the efficiency of research in Indonesian universities and explore performance differences between knowledge areas. Data Envelopment Analysis (DEA) was used to evaluate the efficiency based on the data of 47 universities in the "Mandiri" cluster between 2014 and 2018 and 11 research fields including 10 National Research Priority in Indonesia and one field of mathematics and natural sciences. For this assessment, a total of two inputs and five different outputs were defined. The results showed that the maritime sector consistently had an efficiency value below 1. In addition, the variable, number of employees had more influence on the efficiency value than budget. A significant degree of variety was observed in the difference between the lowest and highest efficiency for each research subject at the Decision-Making Unit (DMU) level.