An investigation was opened in 2014 into the UberPOP application which is used to put paying clients in contact with cheaper, non-professional drivers who do not face the same regulations as cabbies.
Uber France said in a statement that its director general Thibaud Simphal and director for Western Europe Pierre-Dimitri Gore Coty were being interrogated by police after "spontaneously handing themselves in" to police.
"Both of them were taken into custody," said Uber.
Uber has faced rising anger in several countries, particularly in France where a taxi strike last week turned violent as drivers set fire to vehicles and blocked highways, creating a headache for thousands of tourists.
In March a raid on Uber's Paris offices as part of the investigation saw police seize cellphones, computers and documents.
UberPOP has been illegal in France since January, but the law has proved difficult to enforce and it continues to operate.
Licensed cabbies say Uber is endangering their jobs by flooding the market with low-cost drivers.
The taxi strike in France last week saw some 3,000 cabbies block access to the capital's Charles de Gaulle and Orly airports.
Ten people were arrested, seven police officers were injured and 70 vehicles were damaged in clashes between Uber drivers and taxi drivers.
And on at least two occasions in Strasbourg in eastern France last week, taxi drivers posed as customers in order to lure Uber drivers to isolated spots where they were assaulted by cabbies and their vehicles damaged.
'Not above the law'
Didier Hogrel of the FNDT national taxi union welcomed the news that the two Uber bosses were being questioned, saying it showed the good will of the government and justice system."
Alain Griset of the UNT taxi union called for the two men to be sentenced for inciting "undeclared employment."
"They are not above the law, they must understand that the law applies to everybody," he said.
San Francisco-based Uber, which offers several types of ride-sharing services, claims to have 400,000 users of its low-cost UberPOP service in France.
Uber has become one of the world's most valuable startups, worth an estimated $50 billion (roughly Rs. 3,18,760 crores), as it has expanded to more than 50 countries.
But it has faced regulatory hurdles and protests from established taxi operators in most locations where it has launched as it moved from chauffeur service to more informal car-sharing.
Uber has been hit with court injunctions in Belgium, the Netherlands, Spain and France, and has faced protests from taxi firms in numerous major European cities, including London and Brussels.
In France its UberPOP drivers do not pay social charges, do not need to undergo the 250 hours of training mandatory for French cabbies and do not require the same insurance as taxis.
The French investigation is also targeting Uber for allegedly keeping private data for longer than is allowed under a 1978 information law.
Uber has contested the probe and has filed complaints with the EU against France, Germany and Spain for trying to shut it down.
Hungary became the latest country to crack down on ride-booking app Uber, with the government confirming Friday that only licensed taxi drivers would be able to use the service from 2018.
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