Interior Minister Ahmat Bachir said if the six were found guilty, they would face up to 20 years in jail with hard labor.
A judge in the eastern city of Abeche, also upheld prosecutors' charges of complicity against three French journalists, said Justice Minister Pahimi Padacket Albert.
A seven-person flight crew also would be charged with complicity, he told The Associated Press. The British Broadcasting Corp. reported the flight crew were of Spanish nationality.
Authorities in Chad detained 17 people - nine of them French - after the French charity tried to put the children on a plane last week.
L'Arche de Zoe, or Zoe's Arc, said it had arranged French host families for the children to save them from possible death in Darfur. More than four years of conflict there has left more than 200,000 people dead and 2.5 million displaced - many to eastern Chad.
The BBC reported, however, that United Nations sources had privately contested the French suspects' claim that all the children were orphans from Darfur. According to a Monday report by the British media outlet, staffers from the U.N. children's agency UNICEF said many of the kids involved said they came from villages in Chad.
UNICEF's representative in Chad, Mariam Coulibaly Ndiaye, told the Associated Press that authorities were interviewing the children to learn more about their origins.
Gilbert Collard, a lawyer for the group, said the charges against his clients were less severe than he had feared, given harsh comments by President Idriss Deby about them.
"Now we are going to work with Chadian lawyers and contest all the elements against them, one by one," he said. "We are entering difficult territory, but one that is now clearly defined."
French President Nicolas Sarkozy called Deby this weekend to discuss the case, which unfolded as the EU prepares a peacekeeping force in Chad and Central African Republic to help refugees along their borders with Darfur.
France has led the push for the peacekeepers, and the uproar over the charity's actions risked complicating efforts to ensure a smooth start for the force, which Chad initially had resisted.
But Chad has assured France that a debacle over a charity's effort to spirit children out of the country will not affect plans to deploy European Union peacekeepers there to protect refugees from neighboring Darfur, a French official said Monday.
"Because this affair has nothing to do with the deployment of the multidimensional force, there are no possible consequences," France's minister for human rights, Rama Yade, told Europe-1 radio. "And Mr. Deby assured us of that."
In France, police searched the charity's offices as well as the apartment of its founder as part of an inquiry into whether the group broke adoption laws, police officials said. The group initially promised some families that they could adopt - not merely host - children from Darfur, French officials have said.
French diplomats said they had warned Zoe's Ark for months not to go through with its plans. Christophe Letien, spokesman for the charity, insisted its intentions were merely humanitarian.
"The team is made up of firemen, doctors and journalists," he said at a news conference. "It's unimaginable that doubts are being cast on these people of good faith, who volunteered to save children from Darfur."
Two of the detained journalists were covering the operation and a third was reportedly present for personal reasons, according to the media watchdog group Reporters Without Borders. Sarkozy insisted during his conversation with Deby that the journalists' status must be respected, the Foreign Ministry said.
Seven Spanish citizens who work for a Barcelona-based charter airline also were detained in the case, as was a pilot from Belgium, the two countries said. The Chad justice minister made no mention of the Belgian citizen, whose legal status in the country wasn't known.