Chadian authorities will charge nine French nationals with abducting children and fraud, a prosecutor said.
Those charged attempted to fly 103 African children out of the country to live with European families.
Seven Spanish charter plane crew members and two Chadians would be charged with being accessories to the crime, said Ahmat Daoud, public prosecutor in the eastern city of Abeche, where the group were arrested on Thursday.
The accused include the president and other members of French organisation Zoe's Ark, which said it intended to help the children, not abduct them, and that it acted legally.
The children were to be housed in host families who paid the group several thousand euros each.
Zoe's Ark said the operation offered a better life to orphans from Sudan's war-torn Darfur region, many of whose people have fled over the border to camps in Chad.
A lawyer for Zoe's Ark accused Chad's government of using the situation for political ends. He said the children were from a region on the border between Chad and Sudan, adding: "We are unable to tell which country they are from."