The move comes after a Dutch judge convicted three taxi drivers belonging to Uber's low-cost service UberPOP of ferrying passengers without a permit and slapping each with USD 1,600 fine.
"Uber is now a suspect in light of the judge's verdict," the Public Prosecutor's office announced in a statement.
"This means launching a preliminary investigation to gather detail to determine whether Uber is guilty of commercial organisation of illegal passenger transport," the statement added.
Uber said it would contest the ruling and continued to offer UberPOP.
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The Dutch government has since handed more than 50,000 euros in fines against Uber, Dutch media reported today.
Uber uses mobile phone apps to put customers in touch with private drivers who then take them where they want to go, at prices lower than those of traditional taxis.
But despite its growing popularity, Uber is facing increasing limits on its activities in EU countries and a barrage of legal challenges spurred on by a furious taxi lobby, who say Uber drivers should be regulated the same way as normal cabs.
Uber said efforts by national governments to shut it down breached EU laws on competition and the single market.
If Brussels finds EU rules have been violated, it can launch in-depth investigations that could ultimately bring penalties and fines against the national governments.