Ursula von der Leyen said the prime minister is “settling for less” and that he should be “way more ambitious”.
In a major speech last week, Johnson first circulated the idea of reaching an “Australian-style” deal with the EU by the end of the transition period, in which the government will negotiate its future relationship with the bloc.
But no free trade deal exists between Australia and the EU.
It meant critics, such as EU trade commissioner Phil Hogan, immediately picked up on the rhetoric as code for a no-deal Brexit, with the UK trading with the EU on World Trade Organization (WTO) terms. This was the outcome favoured by many hardline brexiteers in Mr Johnson’s Conservative Party.
Ms Von der Leyen had a pop at Johnson in the European Parliament on Tuesday, telling MEPs: “I was a little bit surprised to hear the prime minister of the United Kingdom speak about the Australian model.
“Australia, without any doubt, is a strong and a like-minded partner. But the European Union does not have a trade agreement with Australia. We are currently trading on WTO terms.
“And if this is the British choice, we are fine with that – without any question. But in fact, we are just in the moment where we are agreeing with Australia that we must end this situation, and we work on a trade deal with them.
“Of course, the UK can decide to settle for less. But I personally believe that we should be way more ambitious.”
But Ms von der Leyen also said Mr Johnson’s speech in Greenwich was “an encouraging starting point” with his “ambition” on policies such as the minimum wage and cutting carbon emissions.
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Meanwhile, EU chief negotiator Michel Barnier has warned it would not be “business as usual” after 31 December, when the transition period ends.
He said: “Come what may, on January 1 we will be imposing checks on all products entering the single market, just as we do to every other third country in the world.”