From 1992 to 1998, Nebres was Chairman of the Project Advisory Group for a World Bank- and OECF-financed Engineering and Science Education Project of the Philippine Department of Science and Technology. From 1994 to 1998, he directed a team for the Philippine Department of Education on the development of education plans to strengthen elementary and secondary education in the poorest provinces of the country. He has served as Chair of the Technical Panel on Science and Mathematics of the Commission on Higher Education (CHED) since its inception and also chairs the CHED Technical Working Group for faculty development.