"The Commission has concerns that the companies concerned may have violated European antitrust rules that prohibit cartels and restrictive business practices," the Commission said in a statement.
It did not however indicate which bourses were targeted saying only that the companies probed were "active in managing power exchanges in several [EU] member states."
Confirmation of the Commission's "unannounced inspections" came later from the parties concerned.
"Yes, our office was searched today," said a spokesman for Paris-based electricity exchange EPEX Spot. "We expect the raids were carried out in relation to our cooperation with Nordpool Spot."
EPEX Spot and Norway's Nordpool Spot, which offer short-term electricity trading platforms for French, German, Austrian, Swiss and Scandinavian power, in September announced plans to create a joint exchange which would cover more than half of Europe's spot electricity trades.
EPEX Spot and Nordpool Spot both said they were cooperating with the authorities to ensure they obtained all relevant information.
The two exchanges have a combined annual transaction volume of nearly 600 terawatt-hours (TWh), more than half of Europe's total volumes, and trade in Germany, France, Austria, Switzerland, Norway, Sweden, Finland, Denmark and Estonia.