Interior Minister Claude Gueant said that the 24-year-old man had made several visits to Afghanistan and Pakistan and had said that he was acting out of revenge for France's military involvement overseas Reuters reported.
"He claims to be a mujahideen and to belong to al Qaeda," Gueant told journalists at the scene of the siege.
"He wanted revenge for the Palestinian children and he also wanted to take revenge on the French army because of its foreign interventions," Gueant said.
Heavily armed police in bullet-proof vests and helmets cordoned off the residential area where the raid was taking place, in a suburb a few kilometers from the Ozar Hatorah Jewish school where Monday's shootings took place.
Reuters witnesses at the scene heard several shots at about 0440 GMT.
Gueant said that police were also talking to the brother of the gunman, who is a French citizen from Toulouse.
Police sources told Reuters that a man had been arrested earlier on Wednesday at a separate location in connection with the killings.
The gunman's mother had also been brought to the scene of the siege in a northern suburb of Toulouse to help with negotiations, Gueant said.
"Negotiations with the suspect are ongoing, gunfire has been exchanged," the minister said.
He said that France's President Nicolas Sarkozy had been informed of the situation at 03:00 a.m. (0200 GMT), when the raid began.
Authorities believe that the gunman in Monday's school shooting is the same person responsible for killing three soldiers of North African origin in two shootings last week in Toulouse and the nearby town of Montauban.
The same Colt 45 handgun was used in all three attacks and in each case the gunman arrived on a Yamaha scooter with his face hidden by a motorcycle helmet.
The killings come just five weeks before the first round of France's presidential elections in which immigration and Islam have been major themes as Sarkozy seeks to win over voters from far-right leader Marine Le Pen.
Source : Afghan Voice Agency (AVA), Kabul