The chief executive of Scotland Food & Drink, which promotes the nation's growing food sector, described the proposals outlined by Home Secretary Priti Patel as "hugely worrying".
James Withers said the slowing of immigration post-Brexit was "already hitting hard".
Those concerns were echoed by Tracy Black, director of CBI Scotland, who said the plans posed “real challenges for businesses in Scotland”.
The UK Government's plans will effectively close the door on “low-skilled” immigration from the EU by ending free movement and not issuing visas to migrants who lack qualifications or a job offer in a “high-skilled” profession.
Ministers said the government is delivering on a promise to reduce net migration with a policy that would encourage employers to provide better training and incentives to local and existing workers.
Mr Withers said: "This policy fundamentally misunderstands how our economy works and how crucial immigration is in a country whose population will decrease without it.
"This mustn’t be interpreted as a fear of losing 'cheap labour'. The average salary in Scottish food and drink is double the living wage. This is about our pipeline workforce. There’s many cases of low skilled workers coming to Scotland and now running big operations. We want more.
"The slowing of immigration post-Brexit is already hitting hard. In 2018, 14 of Scotland’s local authorities suffered depopulation. They were mostly rural and island areas, where so much of our farming, food, drink and tourism industries have their foundation."
Ms Black said: “Several aspects of the new system will be welcomed by business, particularly abolishing the cap on skilled visas, introducing a new post-study work visa for overseas students, and reducing the minimum salary threshold from £30,000.
“Nevertheless, the proposed new system will pose real challenges for businesses in Scotland. Key sectors, in particular our vital hospitality, tourism, agriculture and care industries, will be concerned about how they can recruit people across all levels of skill they need, not only to grow but to fulfil existing commitments.
“Against a backdrop of a highly competitive labour market and a declining working age population, employers in Scotland know that hiring from overseas and investing in the skills of their workforce and new technologies is not an ‘either or’ choice - both are needed to drive the economy forward.
The Federation of Small Businesses (FSB) in Scotland has shared concerns over the costs and administrative burdens of the UK Government’s immigration plan.
“When you consider that only five per cent of Scottish small businesses have used the current immigration system, it’s no wonder small employers will be concerned at these plans," said FSB policy chairman Andrew McRae.
"The system is notoriously complex and costly and few small businesses will be able to absorb high administration costs – or have the resources to prepare for new rules in ten months’ time.
“For well-known sectoral and demographic reasons, Scotland’s small employers have a greater reliance on EU workers than the UK average. These staff are central to the success of many businesses in Scotland and therefore it’s crucial that employers encourage them to apply to the EU Settlement Scheme.
“Small businesses need a system that reflects Scotland’s needs without tying them up in red tape. We believe this can be incorporated within a new immigration system if the political will exists. We’re ready to discuss the details in the weeks and months ahead with all concerned parties.”