Philippe Galli, 60, who was named to head the prison service only last year, "presented his resignation on Friday", the ministry said in a statement yesterday.
It gave no reason for Galli's departure but sources within the prison service said Galli and Justice Minister Jean-Jacques Urvoas were badly at odds.
Galli could not be reached for comment. He will be replaced for the time being by his deputy, Stephane Bredin.
Urvoas on Tuesday is to receive a white paper on prisons drawn up by a commission headed by a conservative former senator, Jean-Rene Lecerf.
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The country's jails have been criticised for chronic overcrowding. Social workers say a lack of support for young delinquents makes imprisonment a breeding ground for jihadism.
The number of prisoners reached a record 69,430 on March 1.
Last week the head of a major prison at Villepinte, north of Paris, warned that her facility was already housing twice its capacity and was unable to accept more.
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