By Tom Fairless And Ted Mann 

BRUSSELS--The European Union threw down a hurdle to General Electric Co.'s $17 billion acquisition of France-based Alstom SA's energy businesses, saying it would investigate in detail whether the proposed deal could lead to higher prices for large gas turbines.

Such in-depth investigations by regulators in Brussels aren't unusual and often don't significantly affect proposed tie-ups. But the move injects fresh uncertainty into GE's biggest ever deal, 14 years after EU regulators blocked the U.S. company's $43 billion bid for Honeywell International Inc.

GE beat out a rival offer for Alstom's energy assets from German engineering giant Siemens and Mitsubishi Heavy Industries Ltd. last summer, in a highly public tug of war that roiled the French business world. The deal, a rare instance of a large French company being acquired by a U.S. rival, ultimately required specific approval from the government in Paris.

The European Commission, the EU's top antitrust authority, said Monday it was concerned that the transaction could limit competition in the market for heavy-duty gas turbines, which are mainly used in gas-fired power plants. It said the transaction would eliminate "one of the three main global competitors to GE" in the market--the other being Siemens.

"We are concerned that the proposed acquisition might not only lead to higher prices but also result in less choice for customers and less innovation in the sector," the EU's antitrust chief Margrethe Vestager said in a statement. A final decision on the deal is now due by July 8, the commission said.

A GE spokesman said the company disagreed that the deal could lead to increased prices and less competition for gas turbines in Europe, and said it still aimed to close the transaction by mid-2015.

"We believe...that the gas turbine market is both global and highly competitive," GE spokesman Seth Martin said in an email message. "We disagree with the preliminary concerns raised by the EC statement today and Phase II is the normal process for engagement on these issues."

GE Chief Executive Jeff Immelt told investors in December that the company was aiming to close the Alstom deal by July 1. The company said the July 8 deadline for completion of the European Commission review didn't meaningfully change that timeline.

The EU's decision to focus on the market for heavy-duty gas turbines was widely expected, said Anne MacGregor, an antitrust lawyer with Cadwalader, Wickersham & Taft LLP in Brussels. The regulator is now likely to seek to define the precise geographic scope of that market, to establish the level of competition, she said.

While four large companies compete globally to produce heavy-duty gas turbines--GE, Alstom, Siemens and Mitsubishi Hitachi Power Systems--the commission said the latter seemed to be less active in the European Economic Area than in the rest of the world.

"If the market is really only EEA-wide, and Mitsubishi Hitachi Power Systems is not a strong fourth player in the EEA, that is not a great place to be for the merging parties," Ms. MacGregor said.

Siemens is likely to be "very engaged" with the European Commission as an interested third party, and to have received "bulky questionnaires and other information requests" aimed at teasing out the details of the market, she added.

The commission said the deal was "not likely to raise concerns in relation to power generation equipment for nuclear, coal-fired, wind and hydro power plants, as well as in relation to electricity transmission equipment.

Last month, Alstom Chief Executive Patrick Kron said he expected only "limited overlaps" where European regulators might require that the company divest operations for competitive reasons.

Write to Tom Fairless at tom.fairless@wsj.com and Ted Mann at ted.mann@wsj.com

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