A report says the deal is part of a complex asset swap between Eon and its German rival, RWE, which controls Innogy.
Recently, the commission cleared another part of the deal.
The aim is for RWE to focus on electricity generation and wholesale trade, while Eon centres its business on the retail and distribution of gas and electricity.
According to EU Competition Commissioner, Margrethe Vestager, the commission fears that the deal could reduce competition in gas and electricity retail markets, driving up prices for consumers.
“European households and business customers should be able to buy electricity and gas at competitive prices.
“The in-depth investigation aims to ensure that the takeover leaves sufficient competition in the market to allow for this and does not lead to price increases.
“Initial findings show that Eon and Innogy jointly have a strong market position in Germany, the Czech Republic, Slovakia and Hungary,’’ Vestager added.
The commission expressed concern that the remaining competition would be insufficient to constrain the market power of the combined entity and avoid price increases for consumers.
The commission, the EU’s competition watchdog, now has until July 23 to reach a decision.