Perdue, a Democrat, said she supports shale gas exploration and fracking, but that a measure approved by the Republican-led legislature in June to permit the practices would not ensure adequate environmental protections.
It's the second time in as many years the governor has put the brakes on Republican efforts to push fracking and shale gas exploration in North Carolina, where it is currently not permitted.
In early May, Perdue created a work group to develop guidelines to allow it. The bill approved on a party-line vote a month later would have repealed the ban and established a panel to oversee shale gas exploration.
Perdue said in a veto message she supports energy policies that create jobs and lower costs for businesses and families, but that the state shouldn't act too quickly.
"Our drinking water and the health and safety of North Carolina's families are too important," Perdue said. "We can't put them in jeopardy by rushing to allow fracking without proper safeguards."