The European Commission has opened an in-depth investigation into two joint ventures by aircraft manufacturers Boeing and Brazil's Embraer – a move that has upset plans to close the deal by the end of the year.

The Commission said it is concerned that the joint ventures could reduce competition in the commercial aircraft market.

"Markets for commercial aircraft need to function well to deliver innovative and efficient products to customers at a fair price," EU antitrust chief Margrethe Vestager said in a statement, "We want to make sure that mergers in commercial aircraft do not significantly reduce effective competition on prices and product development."

The Commission has concerns about the creation of two businesses: a joint venture controlled by Boeing that would take over Embraer's commercial aircraft business; and a joint venture controlled by both companies that would be responsible for the Embraer KC-390 military aircraft.

The EU's antitrust team is concerned that the deal could eliminate Embraer as the third-largest global competitor in the commercial aircraft industry.

Boeing has already raised money for the proposed deal through a bond offering, Embraer shareholders and Brazilian antitrust officials have also given approval. Boeing would owe a $100 million break fee if the transaction is felled by regulators. U.S. antitrust officials have raised no objections to the deal.

Boeing and Embraer said they now expect the transaction to close in early 2020.

Vestager's investigation will focus on single-aisle commercial aircraft. Boeing and Embraer compete for the same customers in the market for smaller-aircraft segment – those that accommodate 100-150 passengers. In the overall market for single-aisle aircraft, the Commission believes that Embraer's presence moderates prices despite its small market share. It said it is concerned that eliminating Embraer from the market could remove a force for greater competition.

The Commission will announce the result of its inquiry by February 20 next year.

Under EU competition rules, Vestager can block the merger or require the companies to sell off part of their businesses to reduce any potential reduction of competition.