Nine French and seven Spanish nationals were arrested just over a week ago in the eastern town of Abeche, near the border with Sudan's Darfur region.
In all, 17 Europeans and four Chadians have been charged in the case.
Six of the French are members of Zoe's Ark.
The charity said it was rescuing orphans from Darfur, but UN humanitarian agencies and the Red Cross have since suggested that most of the children are actually from Chad and may not be orphans.
'Operation Children Rescue'
The group in court on Saturday comprised three French journalists, four Spanish flight attendants, three Chadians and Eric Breteau
At the hearing, Breteau said that only he and his fellow charity workers were responsible for the operation, a source close to the case said.
"He [Breteau] said he and his five colleagues were responsible for operation Children Rescue. Neither the French journalists nor the Spanish air crew were involved," said the source.
On Thursday, Idriss Deby, the Chadian president, said he hoped the journalists and the Spanish flight crew members could be released soon.
In Madrid, a spokeswoman for Spain's foreign ministry said the Spanish government was hopeful of receiving "some good news" about the possible release of the airline staff.
But the incident has embarrassed France, Chad's former colonial ruler, and angered many in Chad.
Protests against Zoe's Ark have taken place in both Sudan and Chad, with a crowd gathering outside the court building on Saturday, protesting against the European's alleged kidnap plans.
"An act like this is inhumane. We can't accept this. We must try them here," said Firmin Sanda, a local resident in the crowd.
In France, Francois Fillon, the French prime minister, has asked Bernard Kouchner, France's foreign minister, and Herve Morin, the defence minister, to investigate the case.
It was important to find out how the group "was able to hide its identity on the ground," Fillon wrote in a letter to both ministers.
Meanwhile, about 100 people, some carrying flowers, took part in a silent march in the southern French city of Marseille in a show of support for the Europeans.
Another march is planned in Paris on Sunday.