Brussels has poured cold water on Boris Johnson’s claim to have negotiated an entirely new Brexit deal with the EU, and insisted that it never reopened the withdrawal agreement for him.

A spokesperson for the European Commission raised eyebrows on Wednesday by insisting that the EU had merely made “clarifications” to Theresa May’s Brexit deal and that it had not been “amended” in any meaningful way.

The sensational claim is at odds with Downing Street’s presentation of negotiations: the prime minister hopes to get his agreement through parliament on the basis that it is not the same as his predecessor’s, which was rejected three times by MPs.

“I’m not aware that we have amended the withdrawal agreement,” a European Commission spokesperson told reporters on Wednesday afternoon. “We have certainly made clarifications, but not amended.”

Whatever the Commission says, there are in fact undeniable differences between the withdrawal agreement struck by Theresa May and the one negotiated by Boris Johnson.

The Northern Ireland backstop negotiated by Ms May would have kept the whole of the UK inside the EU’s customs territory, while its replacement does not.

Under the newly negotiated arrangement, Northern Ireland would de facto be inside the EU customs territory, though technically it would not. The new agreement puts a customs border down the Irish sea, and the old agreement did not.

There is also a unilateral exit mechanism for Northern Ireland to leave the proposed arrangement, which did not exist before.

Brussels for months insisted it would never reopen the withdrawal agreement it stuck with Theresa May, so the Commission’s latest claim may be about trying to retain credibility. The EU claimed again in October that it would not reopen the new withdrawal agreement in the current Brexit extension.

Boris Johnson in Brussels with Jean-Claude Juncker, the European Commission spokesperson (Reuters)

When it was pointed out to the European Commission spokesperson that there were obvious differences between the two agreements, and that six paragraphs of the protocol on Northern Ireland were changed, she said there were differing views about what constituted an amendment.

The spokesperson added: “But what matters now is the latest European Council decision on 29 October which excludes any further reopening of the withdrawal agreement that we have spent negotiating for two years, and on the basis of which we granted an extension.”

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It comes after Jean-Claude Juncker, the outgoing European Commission president, said he thought it would be unrealistic to negotiate Brexit changes in six months and put them to a referendum, as Labour has proposed. Mr Juncker however admitted that it would be up to his successor to judge whether there was “room for manoeuvre for a new deal or a new treaty”.