The hostage-taker, identified as Fabrice Boromee, was considered so dangerous when he arrived at Vendin-le-Vieil jail in May that those in charge of keeping watch over him were given special protection gear, unions representing prison workers told AFP.
In an interview with a French TV channel in June, the prisoner had said he was desperate to return to the French overseas territory of Guadeloupe, his home.
He was reportedly jailed in 2010 in Guadeloupe for a scooter theft that turned violent, and was later transferred to mainland France.
He seized the deputy governor, identified as Fabrice Bels, at around 11:00 am (0900 GMT) in the jail's isolation unit.
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Authorities in the Pas-de-Calais region and union sources said Boromee was thought to be armed with a home-made weapon and security forces had gone to the prison to "carry out negotiations and a possible intervention."
Bels was later released safe and sound, officials said. It was unclear whether Boromee had given himself up or whether police had overpowered him.