Dr. Ester Garcia, CHED chair, said the courses fell short of the Standards of Training, Certification and Watchkeeping (STCW) which serves as the "bible" of international seafaring industry.
"These schools can no longer accept first year students for these programs. Currently enrolled students will be assisted to transfer to CHED-recognized schools," she noted.
CHED abolished 23 Bachelor of Science in Maritime Transportation courses and 21 Bachelor of Science in Marine Engineering courses.
A technical panel, composed of experts from CHED and the academe, has been evaluating all the maritime schools in the country to ensure the quality of maritime graduates.
Records showed that 56 maritime courses were found to have fully complied with the standards.
The Philippines had succeeded in its bid to be included in IMOs White List which gives foreign ship owners the go-signal to hire Filipino seafarers.
Garcia added that the phased-out programs can be re-opened the next school year when they have fully complied with the STCW and CHED requirements.