Helric Fredou, 45, shot himself in his office with his police-issue gun on Wednesday night in Limoges, a city in central France, according to France 3.
Commissioner Fredou began his career as a police office in 1997 and had been the deputy director of the regional police since 2012.
Colleagues told France 3 he was "depressed" and overworked, and said he was single and had no children.
A person holds a 'Je Suis Charlie' sign in solidarity with the massacre victims. Photo / AP
Brothers Cherif and Said Kouachi shot 12 people dead at the Charlie Hebdo offices on Wednesday before seeking refuge in a print works.
They were killed on Friday afternoon during a shoot-out with police, as was their alleged accomplice, Amedy Coulibaly, who killed four hostages at a kosher supermarket in Paris.
A statement the morning after the death read: "It is with great sadness that we were informed this morning of the death of our colleague Helric Fredou, assigned as Deputy Director of the Regional Service Judicial Police in Limoges.
"On this particular day of national mourning, police commissioners are new both hit hard by the tragic death of one of their own.
"The Union of Commissioners of the National Police would like to present its most sincere condolences to the relatives of Helric.
"In these difficult times, we have a special thought for all his colleagues and classmates, many of which we expressed their emotion and grief.
"We will keep you informed of how his funeral will be organised and the initiatives we take to honor his memory and support his family."
In the days after the Charlie Hebdo attack, which left police officer Ahmed Merabet dead, the union said it was in a "war" with religious fanatics and would do everything in its power to defeat them.
A statement added: "We are proud of the courage of our colleagues and comrades, who facing seasoned and heavily-armed fanatics have tried at all costs to protect and assist our citizens at risk.
"[Armed officers] managed, with exceptional courage and self-sacrifice, to enable the release of hostages despite abominable complexity."
Newspaper to publish Muhammad images
Surviving Charlie Hebdo staff have revealed this week's edition - to be published on Wednesday with a circulation of 1 million, up from the usual 60,000 - will contain pictures of Muhammad.The surviving members of the magazine's staff decided to print images of the holy figure in defiance of Muslim extremists who slaughtered their colleagues. The cover will be unveiled tonight.
Lawyer Richard Malka said this week's issue will "of course" contain images of the Prophet.
Mr Malka told France Info radio: "We will not give in. The spirit of 'Je Suis Charlie' means the right to blaspheme."
He added: "We will not give in otherwise all this won't have meant anything. A 'Je Suis Charlie' banner means you have the right to criticise my religion, because it's not serious.
"We have never criticised a Jew because he's a Jew, a Muslim because he's a Muslim or a Christian because he's a Christian.
"But you can say anything you like, the worst horrors - and we do - about Christianity, Judaism and Islam, because behind the nice slogans, that's the reality of Charlie Hebdo."
Demonstrators showing solidarity with the Charlie Hebdo victims have also held banners declaring 'Je Suis Ahmed' - in honour of the Muslim police officer Ahmed Merabet, who the Kouachi brothers mercilessly gunned down last Wednesday.
Footage of the officer lying injured on a pavement and raising his arms in defence, before one of the gunmen shot him dead at close range, caused horror and outrage around the world.
During an emotional news conference on Saturday, Mr Merabet's brother Malik broke down when asked about graphic images.
"He was committed," he said. "He looked after his mother and his close family. He was a pillar of the family. He was a very protective father, a lovely brother, a loving companion.
"I am addressing myself to all racists - the Islamophobes and the anti-Semites: You must not mix up extremism with Muslims.
"The madmen have no colour nor religion. Stop ... having wars or burning mosques or burning synagogues because you are attacking people."
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