Clark said she met with the head of WorkSafeBC on Thursday morning and told him investigative shortcomings in the organization "must be fixed."
Clark's comments come as the province released a report entitled The Babine Explosion Investigation: Fact Patterns and Recommendations, looking into the investigation.
Vancouver lawyer Len Doust has been hired as an independent legal advisor to ensure WorkSafeBC investigation issues are fixed according to the report's recommendations, said Clark.
Two people were killed and 19 others were seriously injured when an explosion destroyed the Babine Forest Products sawmill in Burns Lake in January 2012.
Investigation guidelines not followed
In January of this year, Crown prosecutors said that because the WorkSafeBC investigation didn't follow certain guidelines, no criminal charges could be laid.
Provincial Crown counsel spokesperson Neil Mackenize said WorkSafeBC did not follow the rules for conducting a criminal investigation and that would likely result in a significant amount of evidence having to be thrown out.
Those rules included obtaining a search warrant to gather evidence, and warning officials of their rights.
In a written statement, WorkSafeBC responded that it conducted its investigation under the Workers Compensation Act, as it has for many other cases involving injury and death.
It points out the remaining admissible evidence supports a number of potential offences under provincial law, including the theory the explosion was linked to an accumulation of sawdust in the mill.
Following the fire and explosion, the B.C. Safety Authority, a separate independent agency that monitors the safety and licensing of technical systems and equipment, investigated and issued nine recommendations about wood dust management. It also called for improvements to natural gas and propane codes.