Chadian President Idriss Deby Itno has called for an end to demonstrations against all foreign nationals.
This increased tension comes weeks before Irish troops are expected to be deployed to the eastern part of the country.
The protests, particularly in the capital, N-Djamena, are taking place after an attempt by a French charity to take a group of young Chadian children to France.
The EU force will help secure refugee camps along the border with Sudan's Darfur region. Chad's former coloniser, France, will provide the bulk of the 4,300-strong EU force.
In addition, the United Nations will dispatch police to help secure the camps.
Meanwhile, the leader of the Zoe's Ark organisation, Eric Breteau and his partner Emilie Lelouch, have told a Chadian judge investigating the case that they believed they had been rescuing orphans from a war zone.
The pair and four other French nationals face possible sentences of five to 20 years of forced labour if found guilty of trying to fly 103 children to Europe without authorisation.
