A coalition of European and U.S. unions claims that the company reduced its tax burden by moving its British headquarters to Switzerland and channeling money into a Luxembourg-based subsidiary with a Swiss branch.
The unions said the Luxembourg subsidiary, where 13 people work, had revenues over the five-year period of 3.7 billion euros and reported paying just 16 million euros in taxes.
The Commission's move is one of a series in the wake of the so-called LuxLeaks allegations about sweet deals for multinationals with offices in Luxembourg.
The Commission opened tax probes last year into Apple in Ireland, Starbucks in the Netherlands and Amazon in Luxemburg.
Read MoreEU tax probes for Apple, Amazon delayed
It believes that some multinationals are shifting profits between countries and depriving EU governments of tax revenues.
To tackle the problem, the EU has been working on new legislation that would require countries to automatically exchange information on their "tax rulings" every three months.
Tax rulings are the confirmation or assurance that authorities give to tax-paying companies on how their taxes will be calculated.
EU countries rarely share information about their tax decisions and are often unaware of rulings made by their partners, which creates a gap that some multinationals have exploited.