Uber's director general, Thibaud Simphal, and Pierre-Dimitri Gore Coty, director for Western Europe, were both held for interrogation by police on Monday. Authorities said that they were being questioned over "illicit activity".
Bernard Cazeneuve, France's miniser of the interior, has said that Uber's service is "illegal" and has ordered police to keep it off the roads.
The arrests follow a raid on Uber's Paris offices in March, during which police took computers, mobile phones and documents.
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.
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.
Licensed cabbies say Uber is endangering their jobs by flooding the market with low-cost drivers.
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, 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.
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.
US rocker Courtney Love was caught up in the chaos and tweeted that protesters "ambushed" her vehicle and "were holding our driver hostage".
The widow of Nirvana frontman Kurt Cobain condemned "unacceptable violence in a democracy, in a country like France" and said she would be "safer in Baghdad."