The Scottish Government launched a consultation on designating at least 10 per cent of Scottish seas as Highly Protected Marine Areas (HPMAs) by 2026, with a view to selecting sites in 2025.
The Comhairle nan Eilean Siar is formally opposed to the proposals, and Shetland Islands Council has expressed ‘significant concerns’.
From within Mr Yousaf's own party, the SNP MP for Na h-Eileanan an Iar Angus MacNeil called on the new First Minister to drop the plans.
Last week Mr MacNeil wrote to the Minister for Environment and Land Reform, SNP MSP Mairi McAllan, to stress the strength of feeling against the proposals in the islands.
Mr MacNeil said: “There is not a person I know who is in favour of HPMAs. In fact, many people fear for their livelihoods if the plans go ahead.
“HPMAs will cause further economic misery which will do nothing for the environment given that the areas that they want to protect are those that are already fished and looked after sustainably.
“Some people say, 'A new broom sweeps clean' so the new First Minister has a chance to sweep away the clutter of the past and the HPMAs would be a good place to start.”
From the party's opposition, the Conservative Highlands and Islands MSP Donald Cameron also urged Mr Yousaf to drop the plans.
“We all want to do more to protect our environment, but I believe that these plans could have a catastrophic impact for our fishing industry, particularly the nephrops sector, and have a negative effect on many costal communities," Mr Cameron said.
“The commitment may well have been made as part of the Bute House Agreement. But many of my constituents, as well as a number of organisations and businesses, have expressed legitimate and significant concerns about the unintended consequences.
“I appreciate Humza Yousaf is just in the door, but dropping these plans would be a sign to the people of the Highlands and Islands that he is on their side.
“The Scottish Government must look towards evidence-based ways of protecting and enhancing our marine environment, while also supporting our vital and varied fishing industry and coastal communities in general.”
In a defence of HPMAs, Ariane Burgess, Green MSP for the Highlands and Islands, said: "David Attenborough’s Wild Isles series is broadcasting an unavoidable message: the UK’s nature is in trouble, but we can still save it if we act now.
"And the IPCC report published last week rang the alarm bells louder than ever: the window to avert catastrophic climate change is narrowing.
"Globally, there is a renewed focus on protecting and restoring marine habitats, as shown by the High Seas Treaty and the commitment by many governments, including Scotland’s, to protect 30 per cent of our land and seas for nature by 2030.
"That’s why the Bute House Agreement between the Scottish Government and the Scottish Greens includes a commitment to designate a world-leading suite of Highly Protected Marine Areas (HPMAs) covering at least 10 per cent of our seas.
"The Government is proposing HPMAs that will exclude activities that can damage the seabed and marine wildlife, such as fishing, anchoring and construction; this is currently being explored through a public consultation.
"HPMAs are like savings accounts, with an investment in nature set aside that grows like compound interest. Already in use in other territories, the benefits are being felt not just for nature, but also for coastal businesses that benefit from increased tourism, diving and water sports, nature spotting trips and more, and for nearby fisheries.
"In England's Lundy Island No Take Zone, there is evidence of increased tourism spend and of larger lobsters which benefit the nearby shellfish fishery. And in Scotland’s own no take zone in Arran, nursery habitats are recovering, supporting the recovery of
commercially important fish stocks.
"The consultation is looking at how we can support fishers to adapt and thrive. What mitigations are needed to help marine industries adapt, could we nest HPMAs within existing MPAs, and can we ensure the sites are co-managed, as the Arran site is so successfully?"
The proposals are currently under consultation with a closing date of Monday April 17.
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