The inquiry will take 90 days with a final decision expected on 8 July.
EC commissioner in charge of competition policy, Magrethe Vestager, said: "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."
GE acquired Alstom's power business in June in a €12.35 billion deal. As part of the merger, Alstom's offshore unit will be jointly owned by GE and Alstom.
Alstom's onshore wind business will fall under the sole control of GE.
The deal will also see GE takeover Alstom's heavy duty gas turbine business. The commission's main concern is that by having one fewer gas turbine manufacturer would cut competition and increase prices in the sector.
Currently, the EC believes the rest of the merger agreement is unlikely to raise concerns, including the wind power businesses.
The merger was approved by the French government in November.