Meanwhile, in N'Djamena, hearings have begun of four Chadian involved in the case who are being charged with "complicity to kidnap minors and fraud".
Sarkozy recently flew to Chad to pick up three French journalists and four Spanish flight attendants who were among 17 Europeans arrested as they tried to fly the children out of the country.
He said he would "bring back those who stayed behind, regardless of what they have done".
Six French nationals are among those charged with kidnapping minors and fraud.
A French lawyer representing members of Zoe's Ark, the charity at the centre of the affair, has also criticised Sarkozy's intervention.
"This declaration makes our life more complicated - and that is also the opinion of our Chadian colleagues," Gilbert Collard said.
He arrived in Ndjamena on Tuesday night to defend the French nationals.
Zoe's Ark says the children involved were orphans from the neighbouring Darfur region.
The Chadians say almost all of the infants have at least one parent and come from the Chad-Sudan border.
The accused face up to 20 years in jail with hard labour if found guilty in Chad. They would get less severe penalties if tried in France.
French opposition leaders have sided with Chad, saying Sarkozy should not have intervened.
Jean-Marc Ayrault, head of the Socialist Party in the lower house of parliament said: "One might say that there is no more government. He is doing everything and at the end of the day ... it was a serious mistake".
Sarkozy's spokesman said the president did not intend to question Chadian independence but had simply repeated his aim to see the French nationals tried at home rather than in N'Djamena, where they are now detained.
"Obviously everything depends on the decisions of the Chadian judicial authorities. One cannot think differently", said the president's spokesman.