The north-east of England and the Midlands will be hit hardest by a new immigration system that would see the vast majority of low-skilled EU migrants barred from settling in Britain, new analysis reveals.

In a sign that the government’s new “global” immigration system could leave some regional economies facing labour shortages after Brexit, the study finds that more than 90% of EU workers currently working in some English regions would be ineligible under the new rules.

Theresa May has pledged to create a new immigration system after Brexit that does not give preferential treatment to EU citizens. It would effectively mean swaths of low-skilled workers from Europe no longer qualify. Businesses have already voiced major concerns about labour shortages.

Ministers have said that access to EU workers could change as part of Britain’s future trade deal with the bloc. However, in principle the cabinet has agreed that all migrants will be treated equally following Brexit. Workers from outside the EU currently have to pass skills and income tests before getting a work visa.

The analysis, by the Institute for Public Policy Research (IPPR) thinktank, finds that some regions will be worse affected than others. It reckons that 94.5% of EU migrants working in the north-east would not qualify under rules for non-EU workers. In the East Midlands, that applies to 89.6%, and in the West Midlands 89.3%. Even in London, the region least severely hit, 60% of EU migrants would not qualify.

Marley Morris of the IPPR said: “Regions outside London are likely to be most adversely affected by the proposed post-Brexit immigration plans. In the north and the Midlands, EU citizens tend to work in lower-paid, lower-skilled jobs, which means they are particularly exposed to strict new thresholds. This shows the need for greater regional flexibility in the UK’s new system. A one-size-fits-all approach is likely to especially jeopardise economic growth outside the south-east. The government should introduce rules that recognise the differing needs of regional economies.”

The government’s Migration Advisory Committee (MAC) recommended a switch to a “global” system. From 2021, after the proposed Brexit transition period, a new system would require migrants wanting to live in Britain for more than six months to obtain a visa. However, May has guaranteed the rights of EU migrants already in the UK, even if no deal is reached.

The MAC report said the EU’s controversial free movement rules had “neither the large negative effects claimed by some nor the clear benefits claimed by others”.

A Home Office spokesperson said: “After we leave the EU, we will take back control of our borders and put in place an immigration system that works in the interests of the whole of the UK. We commissioned this report … to better understand the impact of EU citizens on the UK labour market. The government is clear that EU citizens play an important and positive role in our economy and society and we want that to continue.

“We will carefully consider the Migration Advisory Committee’s recommendations before setting out further detail on the UK’s future immigration system.”