The deal coincided with a visit by French Minister for Armed Forces Florence Parly to Jakarta to discuss defence cooperation with her counterpart Prabowo Subianto.
"We are planning to acquire 42 Rafale aircraft," Prabowo said at a news conference on Thursday.
"We started this today with the signing of a contract for six aircraft, to be followed soon with another for 36 with necessary support and simulators," he added.
France and Indonesia also signed a preliminary agreement on joint research and development for two Scorpene submarines, Prabowo said.
Parly said Indonesia's deal was further "proof of French industrial excellence and the operational efficiency of the Rafale combat aircraft."
"Our strategic partnership will benefit from the deepening of our defence relations," she said.
"France is proud to contribute to the modernisation of the armed forces of our partner, which plays a key role within ASEAN and in the Indo-Pacific," she added, referring to the Association of the South-east Asian Nations.
France lost a $A90 billion contract to sell submarines to Australia thanks to the AUKUS pact, which allows Canberra to build nuclear-powered submarines with the help of the US and the UK.
Since then, Paris has been trying to court Indo-Pacific powers, including India and Indonesia.
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