The inquiry will also examine Starbucks’s tax treatment by the Netherlands and the tax arrangements in Luxembourg for Fiat Finance and Trade, a unit of the Italian automaker. Mr. Almunia said corporate tax practices in Britain and Belgium would come under the spotlight, though he mentioned no companies by name on Wednesday.

Ireland said it would contest the premise of the investigation, while Apple said that it had “received no selective treatment from Irish officials” and that it “is subject to the same tax laws as scores of other international companies doing business in Ireland.” Apple also noted that it was the second-largest employer in Cork, an Irish city, and that it had added 5,000 jobs in the European Union in the last three years. “Success and growth come from the hard work of our Irish employees not from any special tax deal with the Irish government,” it said.

In a statement, Starbucks said it complied with all relevant tax rules, laws and guidelines, and was studying the announcement. The Dutch government said it would cooperate with the commission but had “confidence” that no illegal aid would be found in “one specific case” concerning Starbucks. The tax practices questioned by the commission were “robust and based on a thorough assessment” as well as “positive for our business climate,” it said.

In Luxembourg, a spokesman for the Finance Ministry said the government would respond on Thursday. Fiat declined to comment.

The effort by the authorities in Brussels is part of a global assault on loopholes that have allowed giant corporations to use complex tax structures to pay small amounts of taxes.