However, Amad Allam-Mi, Chad's foreign minister, told France's RTI radio that the the rebels had been defeated.
"The battle for Ndjamena is over," he said.
Al Jazeera's Haru Mutasa in Ndjamena said that although the rebels had pulled back slightly, French military officials believed that the Chadian government claims may be premature.
"They assume that the rebels have pulled back to regroup, to get more ammunition and will then come back in," she said.
"Will it be in a day's time, a week's time, a month's time? That's what people are concerned about so they are bringing as many foreign citizens, not just French civilians, as possible to the military base."
Koulamallah said that Deby was trapped at his presidential palace in Ndjamena, surrounded by tanks and armoured vehicles, and that the rebels controlled the rest of the city.
He said that rebels controlled the national radio station as well as both strategic bridges across the Chari River.'Bloody and chaotic'
A foreign aid worker told the Associated Press news agency that the scene on the streets of Ndjamena as "bloody and chaotic" with bodies littering the streets and looters breaking into shops during lulls in the fighting.
There has been no indication of the death toll from the two days of fighting but the international medical organisation Medecins sans Frontieres said it had operated on about 50 people in the capital.
A Paris-based spokesman for the group said the Chadian Red Cross had told MSF doctors that they had counted about 200 wounded people.
Witnesses said that hundreds of people could been seen crossing crossing the Chari River to Kousseri in Cameroon.
Helene Caux, spokeswoman for the UNHCR, said at least 400 had crossed and "people are still coming".
The French army said it had flown 580 foreigners out of Ndjamena to the Gabon capital Libreville, leaving about 320 to be taken out late on Sunday and on Monday from an air base next to the main airport. Sudan blamed
The rebels on the capital's outskirts in about 250 pickup trucks mounted with machine guns after a three-day push across the desert from Chad's eastern border with Sudan.
President Idriss Deby seized power in a Libyan-backed coup in 1990
He went on to win the Chad's first two
multi-party elections in 1996 and 2001
A ceasefire signed between Deby and four rebel groups in October recently collapsed
The largest rebel group, the Union of Forces for Democracy and Development, is led by a former minister who accuses Deby of corruption
Click here for more on Chad's spiral into conflict
Mahamat Ali Abdallah Nassour, a Chadian general, claimed that Sudanese troops were involved in the offensive and called it a "declaration of war" from Khartoum.
Allam-Mi threatened future incursions into Sudan to pursue the rebels.
"Sudan has sent these attackers more than 700km to destroy out capital," the foreign minister said.
"If it is necessary for the security of Chad and for the defence of its integrity, we will go to Sudan."
The Sudanese government denied helping wither side in the conflict.
A UN Security Council meeting called to condemn the attack on the Chadian governmenteneded late on Sunday without a declaration being agreed but Jean-Maurice Ripert, Frances' ambassador to the UN, said he was confident a statement would be passed.
"Chad is the victim of aggression by armed groups that want to take power by force," he said.
"The population of Chad is in danger. Refugees and displaced people are in danger. We decided it was essential that the Security Council act quickly."
Ban Ki-Moon, the UN secretary-general, has called for all parties to end the fighting.