A European Commission spokesperson told reporters in Brussels that the request counted officially, despite Mr Johnson sending an unsigned photocopy in an attempt to circumvent the Benn Act, which forced him to request a delay.
The comments come as a top ally of Angela Merkel said “it goes without saying” that the EU should grant the request.
Downing Street had for months insisted that it had a secret plan to avoid a request using a legal loophole, but the prime minister’s gambit ultimately appears to have been a damp squib.
“President Tusk acknowledged receipt of the extension request on Saturday. And, as he stated, he’s now consulting with the EU27. So for us, this form doesn’t change anything,” the commission spokesperson said.
Asked specifically whether the lack of Mr Johnson’s signature on the letter changed anything, the spokesperson simply replied: “No.”
EU leaders could still refuse to grant an extension, as one requires the unanimous approval of the 27 remaining EU leaders.
But Peter Altmaier, a minister in the German government, told broadcaster Deutschlandfunk: “We have already twice agreed to an extension. I have repeatedly said as my own opinion I am not ideologically opposed to extending again a few days or a few weeks if you then certainly get a good solution that excludes a hard Brexit.
“If the British are to opt for one of the longer-term options, that is new elections or a new referendum, then it goes without saying that the European Union should do it, for me anyway.”
Mr Altmaier went on to describe the question of whether parliament or the government spoke for the UK as a “very difficult topic”, stating that “both represent different positions”.
Meanwhile, the European parliament has decided to shelve plans for a vote on Thursday on the Brexit deal, given the uncertainty in Westminster and the prospects of an extension.
Speaking after a meeting of the legislature’s Brexit Steering Group, coordinator Guy Verhofstadt said: “We will advise to the conference of presidents that there has to be full ratification in Britain before we can do our final vote.”
It is understood that MEPs could be called back for an emergency session to ratify the agreement once and if Westminster has given it the nod.
Mr Johnson sent an unsigned version of the letter specified under legislation to demand a delay, said to be a photocopy. He also sent a cover letter signed by the UK’s ambassador to the EU, who made clear that the first letter was from parliament, not the government.
In a third letter, also sent to EU27 leaders, Mr Johnson disavowed his first letter and said he did not want to delay Brexit.
The EU spokesperson indicated that none of this chicanery had made any difference to whether Mr Johnson had requested an extension.
The Benn Act, which forced Mr Johnson to send the letters, was designed by backbench MPs to avoid a no-deal Brexit by forcing an extension if no deal had passed parliament by Saturday 19 October.
In his accompanying letter, Mr Johnson told the EU: “While it is open to the European Council to accede to the request mandated by parliament or to offer an alternative extension period, I have made clear since becoming prime minister – and made clear to parliament again today – my view, and the government’s position, that a further extension would damage the interests of the UK and our EU partners and the relationship between us.
“We must bring this process to a conclusion so that we can move to the next phase and build our new relationship.”
It is understood that the question of an extension was discussed at length at Thursday’s European Council meeting in Brussels. The EU is expected to wait until the middle of this week before issuing a formal response to the request, however, to watch how action plays out in the House of Commons.
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