Boris Johnson’s government has lost its first parliamentary votes since the snap general election, as the House of Lords inflicted three defeats over Brexit legislation.

The upper chamber voted in favour of EU citizens living in the UK to be given physical documents as proof of their right to stay, once the country has left the bloc.

However, the government staunchly defends its digital system and the votes are likely to be overturned when the Brexit legislation returns to the House of Commons.

The first amendment, backed by a Liberal Democrat peer, would give EU nationals the right to receive a residence document instead of the government’s plan to provide only digital proof. It would also grant them automatic right to stay, instead of having to apply.

The Lords passed the amendment by 270 votes to 229. Moving it, Lord Oates quoted Boris Johnson and other ministers who – when campaigning to leave the EU in 2016 – said there would be “no change” for lawful EU residents, who would “automatically be granted indefinite leave to remain in the UK”.

“Sadly, although a great deal of progress has been made with the settled status scheme, these commitments have not been honoured,” he told the chamber.

The peer added that despite the government’s best efforts, it was inevitable that the system would not reach all 3.6 million-plus EU citizens resident in the UK.

“As a result, possibly tens of thousands of otherwise eligible people may find themselves undocumented and criminalised in as little as 18 months’ time. Inevitably, those most at risk will be the most vulnerable: young people in care, the elderly and the marginalised.”

Lack of physical proof of the right to stay would “inevitably cause” problems for EU nationals with landlords, airline staff and other officials, Lord Oates continued.

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For the government, Baroness Williams of Trafford said it would be wrong and counterproductive to change “a system that is working well” and already provided certainty.

“The EU settlement scheme is a vital part of transitioning the UK from free movement to a new, points-based immigration system that starts in 2021,” she added.

The vote brought a quick response from the government. Home Office minister Brandon Lewis tweeted to say he disagreed with the House of Lords. “The EU Settlement Scheme grants EU citizens with a secure, digital status which can’t be lost, stolen or tampered with. There will be no change to our digital approach,” he said.

Last week the European Parliament passed a resolution warning of “grave concerns” over EU citizens’ rights, expressing fears that safeguards for Europeans living in the UK were being jeopardised by the British government’s policy.

Afterwards, the parliament’s Brexit coordinator Guy Verhofstadt said he had been assured that the UK would not automatically deport EU nationals who failed to meet the registration deadline.

A survey of EU citizens living in the UK carried out by the campaign group the3million found that almost 90% were unhappy about the lack of a physical document proving the right to residency.

The poll published this week revealed that many Europeans remain anxious about their status in the UK, despite the government’s assurances over its registration scheme. “Rather than making EU/EEA and Swiss citizens feel – as the scheme name suggests – settled, ‘unsettling status' would be a much more appropriate name,” the report said.

Home Office figures say that more than 2.7 million people had applied for settled status by the end of December.

Peers also voted against plans to give government ministers powers to decide which courts can depart from European Court of Justice judgements. A third defeat followed when they backed a move to make courts refer cases to the Supreme Court if they envisage departing from EU law.

The House of Commons approved the EU Withdrawal Bill earlier this month without any changes. The legislation is designed to ensure a smooth departure from the EU on January 31, implementing the negotiated divorce deal.

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