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The graduate programs of the College of Engineering includes the Master of Engineering Program, the Master of Science in Chemical Engineering and soon to be offered Master of Geomatics and Disaster Risk Reduction (geoDRR) Program. 
The Master of Engineering (MoE) Program was established in 1995 in collaboration with five other member schools selected from the consortium of Engineering and Science Education Program (ESEP) Schools of the DOST. A non-thesis track program (capstone requirement of special problem or practicum paper), it was originally conceived as a practice-oriented approach to improving engineering education and enhancing the technical expertise of engineering instructors and professionals in the region. It has continually served as a delivering institution of CHED's faculty development programs. Today, it continues to develop the expertise of young engineering faculty members  from the colleges and universities of the region and also the young professionals from the neighboring industries and government agencies in the fields of environmental and energy engineering, as well as industrial systems management.
Xavier University is also given approval by CHED to be a delivering institution for the  Master of Science in Chemical Engineering under the CHED SIKAP program. It is a thesis-track program with two specializations: (1) Pollution Control Engineering and (2) Advanced Energy Technologies. 
Preparation and development works are currently ongoing for the offering of the Master of Geomatics and Disaster Risk Reduction (geoDRR) Program by SY 2022-2023. It would be the major output of the EU-funded geoDRR project of which the College of Engineering and the Agricultural and Biosystems Engineering department of the College of Agriculture are jointly involved, together with universities from Malaysia, Cambodia and Europe. It is a non-thesis masteral program that will cover disaster risk and resilience content from physical and geospatial sciences, engineering disciplines as well as the social science specializations that include management, planning, and a survey of local and international DRR laws and policies. Students will gain knowledge and skills in current disaster risk and resilience research and practice fields, disaster risk drivers, risk communication, and disaster risk reduction strategies, disaster resilience-building theory and practices.