The European parliament could block Boris Johnson’s Brexit deal over the UK’s treatment of EU citizens, its Brexit coordinator has said.

Guy Verhofstadt called for the “remaining problems” with citizens’ rights to be solved before consent could be given by the parliament, which is yet to vote on the agreement.

MEPs are worried that problems with the UK’s settlement scheme for EU nationals could cause problems and leave some citizens with no immigration status.

“Everyone presumes the European parliament will give automatically its consent to the withdrawal agreement. Not if the remaining problems with the citizens’ rights are not solved first,” Mr Verhofstadt said on Wednesday. “Citizens can never become the victims of Brexit.”

Ultimately, Mr Verhofstadt does not control the votes of MEPs in the parliament – so his warning could ring hollow if group and party leaders decide they would rather swing behind the plan.

But his comments illustrate concerns in Brussels and other EU capitals that there could be another Windrush scandal waiting for their citizens who have made their home in the UK.

Ministers have said that EU citizens could face deportation if they don’t make the deadline to sign up for the Home Office’s settlement scheme. The number of exceptions are reported to be relatively narrow, according to lawyers briefed on the plans.

Mr Verhofstadt has previously said that the settlement scheme should be “declaratory” rather than an application process and that the Home Office should have to find reasons to reject people, rather than the other way around.

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While Boris Johnson has almost certainly gained a majority in the UK’s House of Commons for the Brexit deal thanks to his election victory, it must also get past MEPs. The date of the European parliament vote is yet to be decided, though the legislature insists it will take place after the Commons’ own vote.

The House of Commons is expected to vote on the first stage of the bill enshrining the Brexit deal in law on Friday. The remaining Commons stages, and those in the House of Lords, will follow in early January.

The European parliament will then initiate its own processes for ratifying the deal. If it is approved, the UK is expected to finally leave the EU on 31 January.

Mr Johnson centred his successful election campaign on a promise to “get Brexit done”. All Conservative candidates were made to promise to support the prime minister’s exit deal.

Despite the party’s crushing defeat last week, Jeremy Corbyn has said that Labour will continue to vote against the deal. It remains to be seen whether any of the candidates to succeed him will defy his orders in a bid to mark a break with his tenure and show they are committed to winning back Leave-supporting Labour voters.

Home Office minister of state Brandon Lewis said: “EU citizens are our friends, colleagues and neighbours. We recognise the enormous contribution they make to the UK and we want them to stay.

“We have already provided certainty to over 2 million people who have been granted status through the EU settlement scheme. Our scheme is free, there is plenty of support for applicants and more than a year left to apply.