Announcing the move, the EC said it had “concerns that on a number of European markets for international express and regular small packaged deliveries, the merged entity would face insufficient competitive constraints” if the takeover went ahead.
“This could lead to higher prices for business customers and consumers,” it added.
FedEx originally announced its intention to take control of TNT Express in April. The move would create a business with a global turnover of €49.7bn (approximately £35bn), based on 2014 revenues.
Commenting on the decision to investigate, Margrethe Vestager, EC commissioner in charge of competition policy, said: “Many businesses, and in particular e-commerce, relay heavily on affordable and reliable small package delivery services and many consumers depend on these services to ensure rapid and safe delivery of goods they have bought.
"The Commission must therefore make sure that FedEx’s takeover of TNT would not impede effective competition and would not lead to higher prices for consumers.”
The EC has a 90-day period in which to conclude its investigation.