People in the Chadian town of Abeche have been protesting about last week's alleged child-kidnapping attempt.
The women were shouting anti-French slogans
Sixteen Europeans were arrested in the town while trying to fly more than 100 children they believed were orphans from Sudan's Darfur region to France.
Meanwhile, the Chadian government has said aid agencies will be allowed to continue their humanitarian work for Darfur refugees despite the scandal.
It also said it would not hinder the planned deployment of peacekeepers.
A 3,000-strong European Union force is due in the country in the next few weeks to protect Darfur refugees and people displaced in the conflict that has spilled over the border from Sudan.
Nine French citizens were charged with child kidnapping and fraud on Tuesday and seven Spanish air crew were charged as accomplices.
If they are found guilty, the group will face between five and 20 years in prison with hard labour.
Staff from the UN children's agency Unicef say many of the children, now being kept in an orphanage in Abeche, a town near Chad's border with Darfur, cry at night for their parents and say they are from villages in Chad.
The BBC's Stephanie Hancock in Abeche says angry crowds took to the streets to vent their anger about the affair.
The children are not being treated for any serious illnesses or injuries
Some women hurled stones at foreign journalists and shouted anti-French slogans, AFP news agency reports.
"No to the slave trade! No trafficking in children!" they are quoted as saying.
Our correspondent says hundreds of protesters converged at the home of the governor of Abeche waving placards.
"We are here to see that justice will be done in transparency, and here in Abeche, not anywhere else. And to see that children and their parents get their rights," one woman said.
Addressing the crowd, the governor urged citizens not to blame the French as a whole.
The case is extremely controversial - not least because of all the links to France, Chad's former colonial power, our reporter says.
On Tuesday, French Prime Minister Francois Fillon said his government had done all it could to stop the operation by the charity Zoe's Ark from going ahead.
"The foreign minister did all he could to dissuade Zoe's Ark from pursuing this operation, and a judicial inquiry has been open since October into this operation and this organisation," he told parliament.
But the wife of one of those charged, Christine Peligat, said the charity workers only had one objective in Chad.
"They were rescuing children from Darfur, and the only thing they wanted was to give these children a better life. That's it. This is the only aim of this operation," she told the BBC.
Correspondents say there have been worries the affair would damage Chad's relations with France - the main backer of the EU peace force.
But French President Nicolas Sarkozy said he had spoken to his Chadian counterpart Idriss Deby.
"I assured him of the fact that we condemn these activities, and then we are going to try to find agreements so that nobody loses face in this case and so that we find out the precise truth: Why they went to pick up those children and to what end."
In turn, Chad has sought to ease tensions.
"When this affair erupted, the president gave assurances once again to French authorities that this case of transporting children would not call into question the deployment of the European force ... that is clear," Reuters news agency quotes Chad's presidential spokesman Mahamat Hissene as saying.