The hostage-taker, identified as Fabrice Boromee, was considered so dangerous when he arrived at the 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 television channel in June, the then 34-year-old who comes from the French overseas territory of Guadeloupe had said he was desperate to go home.
He took the deputy governor, identified as Fabrice Bels, hostage at around 11:00 am local time in the isolation unit of the Vendin-le-Vieil prison.
Unions added his weapon appeared to be home-made.
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The prison houses some of France's most dangerous criminals -- one of only six in the country to do so -- with some 238 places, although there are currently only 51 inmates in the jail.
It only opened this year and the building contains "highly sophisticated safety features," according to the justice ministry.
According to union sources, Boromee is "very well-known on the prison circuit", having already taken people hostage in 2013 in another French prison where he was an inmate.