Fish habitat is essential to the stability and productivity of fisheries. In Canada, the primary legal tool for protecting fish habitat is the federal Fisheries Act. In 2012, this law was changed to narrow the scope of habitat protection. The government’s position was that the previous regime went beyond what was necessary to protect fish and fish habitat. Here, we tested that assertion by examining Fisheries Act authorizations to harmfully alter, disrupt, or destroy fish habitat issued by Fisheries and Oceans Canada during a 6-month period in 2012, obtained using access to information processes. We found the majority of projects (67%) were authorized to impact more habitat than proponents were required to compensate for, likely resulting in a net loss of fish habitat. Our analysis show an aggregate net loss — defined as authorized impact minus required compensation — of 2 919 143 m2 authorized across 78 projects. Drawing from these results, we present four recommendations for an improved habitat protection regime under a renewed Fisheries Act, emphasizing the need to establish a public registry for authorizations and monitoring data.