One of the sources said that two Mirage 2000D combat jets and a tanker aeroplane took off before 1230 GMT, a French source told AFP. A third took off later.
"The French armies are withdrawing today the fighter jet capability present in N'Djamena," said the French army staff on Tuesday in a statement, referring to the aircraft.
A second source said their presence was "no longer justified after the end of the deal" struck in November.
Chad's Foreign Minister Abderaman Koulamallah, welcome the decision.
"The definitive departure of the Mirage fighter aircraft" marks the "first stage of the disengagement of the French military forces stationed in Chad", before "the gradual withdrawal of the ground forces in the coming weeks", Koulamallah said.
Chad had been a key link in France's military presence in Africa and its last foothold in the wider Sahel region after the forced withdrawal of its troops from Mali, Burkina Faso and Niger in the wake of a series of military coups.
But it announced on November 28 a decision to end a defence accord with Paris mainly dating from independence in 1960.
"The people of Chad aspire to a future where national sovereignty is fully respected," Koulamallah said in his statement.
France until then had about 1,000 troops in the country.
"The conditions of the withdrawal of other French military capabilities present in Chad are being coordinated with the Chadian authorities," said the French army chief of staff.
France has been forced since 2022 to remove troops from Mali, Burkina Faso and Niger after military takeovers that have seen the countries become closer to Russia.
Chad's leader General Mahamat Idriss Deby Itno has also sought closer ties with Moscow in recent months but talks to strengthen economic cooperation have yet to bear concrete results.
The Chadian president has previously said that the defence agreement did not mean "a rejection of international cooperation or a questioning of our diplomatic relations with France, whatsoever".
"They are realising how much they are losing," said one of the French sources, adding that relations were tense between backers of the withdrawal and those opposed for national security reasons.
The landlocked nation faces a potent threat from Boko Haram and other militant groups.
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