The man inside the bungalow where the operation is taking place has claimed affiliation to Al-Qaida, Interior Minister Claude Gueant told reporters.
Two police officers have been reported injured in the operation.
The man's mother has been brought to the scene to aid negotiations, Mr Gueant said.
He added that the man's brother was under arrest.
"He [the suspect] was in the DCRI's sights, as were others, after the first two attacks," an unnamed official told Agence France-Presse, referring to France's domestic intelligence service.
"Then the criminal investigation police brought in crucial evidence," the official added.
Police wearing helmets and flak jackets have cordoned off the residential area of Toulouse where the raid is happening, an eyewitness told the Liberation newspaper.
Other emergency services are also in attendance.
A huge manhunt has been under way in France amid fears the killer may strike again.
FuneralsMeanwhile, the funerals of the rabbi and three children killed in Monday's attack are due in Jerusalem in the coming hours.
Israeli police said they expected thousands of people to attend.
Also on Wednesday, French President Nicolas Sarkozy is to attend a memorial service for three soldiers killed in two attacks last week which police have linked to the Toulouse shootings.
The same gun and the same scooter were used in all the attacks. All three soldiers killed were of North African descent. Another soldier from the French overseas region of Guadeloupe was left critically ill.
The attacker gunned down Jonathan Sandler, a 30-year-old rabbi and teacher of religion, his two young sons Arieh and Gabriel and then - at point blank range - the head teacher's daughter, seven-year-old Myriam Monsonego, in Monday's attack at a Jewish school in Toulouse.
Their bodies were carried out of Ozar Hatorah school on Tuesday in two black hearses and taken to a nearby airport, reported AFP.
A military jet then flew them to Paris, from where they were placed on a commercial flight to Tel Aviv, AFP said. They have now arrived in Israel.
French Foreign Minister Alain Juppe was to accompany the relatives of the dead to the funerals in Jerusalem.
Mr Sarkozy and the Socialist presidential candidate Francois Hollande will attend the memorial service in Montauban for the three soldiers killed in last week's attacks.
Jonathan Sandler and his two oldest children were killed in the school attackMarine Le Pen, the leader of the far-right Front National, will also be at the service.
She is often associated with the more controversial debates on immigration and her presence will be closely observed in light of recent events, reports the BBC's Christian Fraser in Toulouse.
Scarlet alertOn Tuesday schools across France held a moment's silence to remember the victims of the killer, whom President France Sarkozy branded a "monster".
It is the first time in the country's history that the national terror alert has been raised to "scarlet", its highest level.
The measure enables the authorities to disrupt daily life and implement sweeping security measures. These include mixed police-military patrols and powers to suspend public transport and close schools.
Mr Gueant has said the killer had a camera strapped to his chest and may have filmed the shootings.
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