In a book by two journalists from the daily Le Monde published Thursday, Hollande described the justice system as "a cowardly institution", saying "these prosecutors, these senior judges, act all virtuous while keeping their heads down."
The book, based on dozens of interviews with Hollande, contained a raft of embarrassing revelations as he nears the end of his mandate with a re-election bid still hanging in the balance.
"I deeply regret what has been taken as an insult by judges whose courage and devotion to their difficult work I admire every day," the Socialist leader wrote in a letter to the country's top judges, saying the remarks were misinterpreted.
In the letter, hand-delivered by his Justice Minister Jean-Jacques Urvoas to the High Council of the Magistrature, Hollande said the remarks had "no relation to my true thinking."
It was also addressed to the judges' union USM.
Top judicial officials slammed the remarks Thursday as "degrading" and "humiliating".