David Besner, a professional chemical engineer and a former assistant deputy minister with the provincial government, takes the job effective immediately.
Energy Minister Craig Leonard says Besner is a member of the scientific advisory council for the energy institute.
The institute is studying the shale gas industry.
In various biographies, LaPierre said he had a doctorate in ecology from the University of Maine, but the school says it has no record of him earning the degree.
Premier David Alward says the energy institute now has a perceived lack of credibility and work must be done to rebuild its reputation.