Ursula von der Leyen, who took over from Jean-Claude Juncker earlier this month, has said she has “serious concern” over the limited time available for the second round of negotiations.
The EU chief said both sides should keep their options open during the discussions, including the possibility of extending the transition period.
Speaking with the French newspaper Les Echos, she said: “It’s not only about negotiating a free trade deal but many other subjects”.
She added: “It seems to me that on both sides we must ask ourselves seriously if all these negotiations are feasible in such a short time.”
The Prime Minister has said that he will not agree to an extension to trade talks, and has repeatedly claimed that there is enough time to agree to a deal.
After the UK leaves the EU on January 31 next year, it will stay in the single market and customs union until the end of the year while negotiations are held over its future relationship with the bloc.
It will also follow EU rules, accepting rulings from the European Court of Justice, and will continue to contribute to the group’s budget.
This transition period can be extended for a further two years, but it must be agreed by July 1.
Ms Von der Leyen said that July 1 will provide a “moment of truth” in the discussions.
She said: “I believe that it would be reasonable to review things in the middle of the year, if necessary to see if an extension is needed.”
The Commission president also said that there would be disruption and “barriers” if the UK chooses to move away from EU trade standards.
“If we want to benefit from the prosperity of the single market, to access it without barriers or customs duties, we must all accept its common principles and values,” she said.
“Otherwise, the two parties must agree on the barriers to be put in place.”
A government spokesperson said: “The prime minister has been clear that we will not be extending the implementation period.
“Both the EU and the UK committed to agreeing a future partnership by the end of 2020 in the political declaration and have agreed to work with great energy to achieve this.”
In the next two weeks, EU representatives will begin internal discussions about their own negotiating position, looking first at post-Brexit data flows, and then at trade and intellectual property.
