Ms Fuentes went on to say that judges could be told to make rulings in favour of the government under threat of being removed from their positions.
Legal experts have warned that the scale of the overhaul could see major problems in the short term.
“We’re going to see some very bad rulings at the beginning,” said Juan Jesús Garza Onofre, a constitutional law researcher at the National Autonomous University of Mexico.
“There is going to be a learning curve that involves delaying processes that are already underway,” he added.
In August, Ken Salazar, the US ambassador to Mexico, said that the reform was a “major risk to the functioning of Mexico’s democracy”, which led to the Mexican government pausing its relationship with the US embassy.