Ursula von der Leyen said Downing Street’s attempts to override the Brexit treaty with the UK Internal Market Bill had “distracted very strongly” from the two sides being able to secure a deal before the approaching deadline on December 31.
The bill, which looks at how England trades with Scotland, Wales and Northern Ireland post-Brexit, has proved controversial both in and outside of the House of Commons.
It gives the Government power to change aspects of the European Withdrawal agreement – a legally-binding deal which was signed with Brussels in January.
Mr Johnson was forced on Wednesday to agree to table an amendment to the Internal Market Bill, giving MPs a vote before the Government can use the powers related to Northern Ireland which would breach the treaty.
But the compromise has not seen Brussels back down, with Eric Mamer, chief spokesman for the European Commission, telling a press briefing that its position had not changed and it still wanted the offending clauses to be withdrawn from the legislation.
Despite the row over the Bill Ms von der Leyen said she remained sure that consensus on a future partnership with the UK could be reached.
It comes after the former London School of Economics student used her annual State of the Union address to the European Parliament on Wednesday to warn Mr Johnson the UK could not unilaterally set aside the Withdrawal Agreement.
Ms von der Leyen, in comments reported by Politico, told reporters on Thursday: “Where the UK is concerned, we want an agreement, and I think the attempt to violate the Withdrawal Agreement distracted very strongly from the ongoing negotiations.
“This was an unpleasant surprise. And therefore it is time now that our British friends restore the trust in the validity of a signature under treaty, and that we keep on going, focused to negotiate because time is running out.”
In reply to another question, the German politician said she was “still convinced” a deal with London “can be done”.
The commission president’s comments come as the UK confirmed “some limited progress” had been made between the negotiation teams during informal talks in Brussels this week.
“The UK’s negotiating team had useful informal discussions with the EU this week as we seek to reach an agreement by mid-October on our future relationship,” said a UK Government spokesman.
“These covered a broad range of issues and some limited progress was made, but significant gaps remain in key areas, including fisheries and subsidies.
“We will continue to work hard to bridge those gaps in talks next week, without compromising our fundamental position of being an independent country.”
Additional reporting by PA Media.