Margrethe Vestager, the European Commissioner for Competition, told CNBC's Sara Eisen that one of her agency's primary goals in the Amazon investigation to protect consumers by ensuring competition and innovation.

EU regulators are questioning Amazon merchants about whether the company is using seller data to its advantage by replicating and selling its own version of products and undercutting smaller companies on its platform.

"It's too early to have a concern, but we like to understand how this is working because Amazon has this dual role," Vestager said to Eisen. "They host a lot of little guys and at the same time, they're a big guy in the same market. So how do they treat the data that they get from the little guy? Does that give them an advantage that cannot be matched?"

Vestager said that while the commission has heard concerns, it has not received formal complaints of such behavior.

Vestager has the power to fine companies up to 10 percent of their global turnover for breaching EU antitrust rules. Last year, she fined $5 billion because of its Android software and launched an investigation into Apple when it purchased the app Shazam.