Ministers who clap for key workers are “only too happy” to back immigration reforms which suggest thousands are “unwelcome in our country”, according to Labour.

Shadow home secretary Nick Thomas-Symonds said the Government was proposing a new immigration system in the middle of the Covid-19 pandemic which “sends a signal” that anyone earning below £25,600 is “unskilled”.

He dismissed this prospect as he launched a defence of shop workers, refuse collectors and local government staff from overseas for playing their part in the coronavirus response.

His criticism came as MPs considered measures to repeal EU freedom of movement rules in the UK via the Immigration and Social Security Co-ordination (EU Withdrawal) Bill, which cleared its first hurdle after receiving a second reading by 351 votes to 252 – majority 99.

The legislation is part of the move towards the Government’s new points-based immigration system, to be introduced from 2021, although it does not set out the details on this.

These will be fleshed out in the immigration rules, which will explain the future system for EU and non-EU nationals who move to the UK after the Brexit transition period ends on December 2020.

Opening the second reading debate, Home Secretary Priti Patel said the Bill will create a “firmer, fairer and simpler system” that will “play a vital role” in the country’s recovery from coronavirus.

NHS staff, she said, were the “very best of Britain”, adding: “That is why we are introducing a new fast-track NHS visa to prioritise the qualified staff needed to provide high quality and compassionate professional care.

“During these exceptional times, it is right that policies which affect our NHS workers are kept under review including the immigration health surcharge and that’s why I recently announced a free automatic one-year visa extension for those with six months or (less) left to stay on their visas.”

She also said of the Bill: “It delivers on the promise we made to the British people. It ends free movement. It takes back control of our borders.

“It gives the Government the powers needed to deliver an immigration system that is firm, fair and fit for the future, the points-based system the public voted for, a system that will support our economic recovery by prioritising jobs for people here in the UK while continuing to attract the brightest and the best in terms of global talent.”

But Mr Thomas-Symonds said: “In the midst of this crisis the Government is putting forward an immigration system containing a salary threshold of £25,600 – it sends a signal and tells people that anyone earning less than that is unskilled and unwelcome in our country.”

Mr Thomas-Symonds said the earnings of frontline workers do not reflect their contribution to society, adding: “Those who clapped (for carers) on Thursday are only too happy to vote through a Bill today that will send a powerful message to those same people – that they are not considered by this Government to be skilled workers.

“Are shop workers unskilled? Are refuse collectors? Are local government workers? Are NHS staff? Are care workers? Of course they are not.”

SNP immigration spokesman Stuart McDonald criticised the “dreadful” Bill, saying: “It’s a Bill that will result in many thousands of EU nationals losing their rights in this country overnight and which will extend the reach of the hostile environment still further.”

Yvette Cooper, Labour chairwoman of the Home Affairs Committee, said she believes the Bill is “flawed”, but that immigration legislation is needed and she will put forward amendments which she hopes will receive cross-party support.

She went on: “In that cross-party spirit I will not vote against the Bill tonight, although if the Government’s approach does not change, I would expect to oppose it when it returns to the House.”

Labour’s Diane Abbott, a former shadow home secretary, said the Bill is “bad in principle, bad in practice” and described it as a “slap in the face for the thousands of migrants, including EU migrants, working so hard for the NHS and care sector in this time of Covid crisis”.

In February, the Government announced proposals for the new system, with points awarded for specific requirements such as being able to speak English to a certain level, having a job offer from an approved employer and meeting a salary threshold of £25,600.

Other points could be awarded for certain qualifications and if there is a shortage in a particular occupation.

A visa allowing doctors, nurses and health professionals from overseas to work in the NHS was introduced in March.