David Kerfoot, who chairs the York, North Yorkshire and East Riding Enterprise Partnership, has questioned who will fill short term gaps in the tourism, food and agriculture sectors once the proposed points-based system kicks in on January 1.
The changes are designed to cut the number of low-skilled migrants entering Britain but aim to make it easier for higher-skilled workers to get UK visas.
A policy statement outlining a new points-based system after freedom of movement ends said the economy needs to move away from a reliance on "cheap labour from Europe".
Analysis by the IPPR think-tank suggests 69 per cent of the EU workers currently living in the UK would be ineligible for a skilled work visa under the new scheme. But Yorkshire could be worse-hit as 80 per cent of its EU workers would be ineligible.
Mr Kerfoot told The Yorkshire Post: "While I accept there has to be some type of filtering of people who enter the country, over the last decades it's been clear that unskilled jobs are not always popular with our population.
"Our dependency on un-skilled or semi-skilled workers from the EU to fill the gaps is huge. With that ageing population securing care workers is a big task and it’s the practical implications of this, on the ground, which concern me.
"Who will fill this short term gap? How will it be managed? Will there be any government support to help companies through this period of time?
"I completely agree we need to switch away from low paid employment to higher level opportunities but this is going to take time and if we are only being given a year to change then I can foresee challenges on a large scale."
Marley Morris, IPPR Associate Director of Immigration, Trade and EU Relations, said: "Our analysis suggests that the vast majority of EU migrants living in Yorkshire and the Humber would be ineligible for a skilled work visa under the government's points-based system.
"This has major implications for future migration to the region. For local employers looking to hire workers from overseas, the government's proposed skills and salary thresholds are likely to bite particularly hard.
"In social care in particular, there is a risk that the new system could exacerbate pre-existing shortages."
The think-tank called for a regional element to be introduced to the immigration system, with more points awarded to migrants willing to move outside London.
But speaking in Leeds yesterday, Immigration Minister Kevin Foster said the independent Migration Advisory Committee recommended against the use of regional salary thresholds for a skilled visa.
He said: "If you think about it would be somewhat of a nonsense to have a different salary threshold in, say, Leeds as we had in Liverpool and how we would end up enforcing, that could become very complex and difficult."