The announcement came as the U.S. and other fiscally challenged countries have been trying to crack down on corporations funneling profits through foreign subsidiaries to avoid or reduce tax payments.
"In the current context of tight public budgets, it is particularly important that large multinationals pay their fair share of taxes," said Joaquín Almunia, vice president in charge of competition policy for the European Commission.
The investigation will determine whether tax breaks provided by Ireland to Apple, the Netherlands to Starbucks and Luxembourg to Fiat constitute improper "state aid" to the companies, he said.
"Under the EU's state aid rules, national authorities cannot take measures allowing certain companies to pay less tax than they should if the tax rules of the member state were applied in a fair and nondiscriminatory way," Almunia said.
Apple in particular has been criticized for funneling profits through Irish subsidiaries.
A Senate investigation last year concluded that Apple executives negotiated a special low tax rate with the Irish government that allowed the company to avoid paying at least $15 billion in U.S. taxes on $44 billion in foreign income from 2009 to 2012.
"I don't know how you got to have Apple to have so much of their business in Ireland, we thought they were a Californian company," an Irish newspaper quoted California Gov.
"When you look at their tax returns, they're really an Irish company ... it's called creative accounting," the Irish Independent quoted Brown as saying at the event, which included the Irish prime minister. A Brown spokesman said he was joking.
Apple and the Irish government have denied any special treatment.
"Apple pays every euro of every tax that we owe," the company said Wednesday. "Since the iPhone launched in 2007, our taxes in Ireland have increased tenfold."
Ireland's Department of Finance said "the company in question did not receive selective treatment and there was no 'special tax rate deal.' "
Apple Chief Executive
Starbucks also has been under fire for its tax strategies in Europe. In April the company said it would move its regional headquarters from the Netherlands to London after criticism that it was not paying its share of taxes in Britain.
The company said Wednesday that it complied with "all relevant tax rules, laws" and guidelines by the Organization for Economic Cooperation and Development, a group of the world's 34 most advanced economies.
Eric Wiebes, the Dutch state secretary for finance, said Wednesday that he was confident the European Commission investigation would determine there was no improper state aid provided to Starbucks.
The European investigation also involves taxes paid in Luxembourg by Fiat Finance and Trade, a subsidiary of the Italian automaker. Luxembourg is another European Union nation criticized for being a tax haven for large corporations.