Francois Fillon said: "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."
Sixteen workers from France and Spain were arrested in the town, along with two from Chad, while attempting to fly more than 100 children they say they thought were orphans from Sudan's Darfur area to France.
Nine French people were charged with kidnapping the children in Chad and seven Spanish aircrew were charged as their accomplices.
The UN children's agency Unicef say many of the children, who are now being kept in an orphanage in Abeche, say they are from villages in Chad and miss their parents.
