Hundreds of mainly male migrants try to jump on lorries heading onto ferries or to get on trains going through the Channel tunnel to get to Britain.
"When they get out of the jungle, the Afghans are just going to move one or two hundred metres away"
Friar Jean-Pierre Boutoille, aid worker
Immigration ministry officials said "the Jungle" has become a haven for people smuggling gangs and that it had become a virtual "no-go zone".
But aid groups working in the area said that the closure would not stop the would be migrants congregating in Calais hoping to get across the Channel.
"It is ridiculous," Friar Jean-Pierre Boutoille of the C-Sur coalition of aid groups said.
"When they get out of the jungle, the Afghans are just going to move one or two hundred metres away."
The ministry said that dozens of squats inside the zone had been closed over the past six months and that 170 people had made requests for asylum in France.
They estimated that there were about 700 people there three months ago and that there are about 300 now.
Besson said that an "individual solution" would be found for each person in area, including a voluntary return to the their home country, an asylum request or expulsion.
With regard to Afghanistan he said if conditions there "do not allow this there will be no forced return" to this country.
"The closing of the jungle will not be the end of the fight against the underground networks," said Besson, who added that other operations will follow.
French authorities had a centre for migrants at Sangatte, near Calais, but this was closed in 2002 because of similar fears about crime.