This paper evaluates economies of scale and scope, and the merger effect among national universities in Japan. We apply SUR for the total translog cost function in FY2014 and FY2018. The main results are: (i) there exist economies of scale as a whole university; (ii) but there exist no clear economies of scope except for in research; (iii) there are cost saving effects with mergers among single colleges, but not in the case of mergers of general universities and medical colleges, (iv) both the costs of a public and a private university are higher than those of a national university.