The prime minister was urged by a Highland MP to intervene to protect "deeply" concerned constituents.
HPMAs, banning fishing, farming, seaweed harvesting and other human activities in 10 per cent of Scotland's seas, aim to protect and restore marine life for the future.
HPMAs are a key part of the Bute House Agreement - which brought the Scottish Greens into government in a historic power-sharing deal with the SNP.
First Minister Humza Yousaf and Net Zero Secretary Mairi McAllan have said the zones will not be imposed on communities that do not want them.
The issue sparked the first backbench dissent since Mr Yousaf succeeded Nicola Sturgeon as SNP leader.
A rebellion of three former SNP ministers voted against a Scottish Government motion supporting the proposals, in a Holyrood debate on May 3, but the mutiny was defeated by a majority of SNP and Green MSPs.
One rebel, Na h-Eileanan an Iar SNP MSP Alasdair Allan, said: "This is the first time in my 16 years as an MSP that I have voted against the SNP’s collective position on any issue, and I do so with the greatest reluctance.
"There is no buy-in at all across my constituency for these proposals, as they stand."
A second rebel, the SNP MSP for Skye, Lochaber and Badenoch Kate Forbes, warned people, not wildlife, could become the "endangered species" in the Highlands and Islands, in another Holyrood debate on HPMAs the day before.
“I cannot think of a more important issue on which to give my first speech from the back benches since 2018," the former finance secretary said, after losing her SNP leadership bid to Mr Yousaf, and refusing a role in the new First Minister's cabinet.
"Given that it is about conservation, my warning is stark: if the proposals go ahead as planned, the rarest species in our coastal areas and islands will soon be people."
The third rebel, SNP MSP for Inverness and Nairn Fergus Ewing, dramatically tore up the Scottish Government’s consultation paper on HPMAs.
Mr Ewing said: “When I had the privilege of serving as the member of the Scottish Parliament for Lochaber for eight years, I got to know the fishermen in Mallaig and Arisaig.
"The document that I am holding is not a consultation document - it is a notice of execution."
HPMAs were raised a week later at Prime Minister's Questions in Westminster on May 10, by the Lib Dem MP for Caithness, Sutherland and Easter Ross, Jamie Stone.
Mr Stone said: "The Prime Minister may well have seen the astonishing sight of a former Scottish Government Minister standing up in the Scottish Parliament chamber and tearing up—literally, ripping into pieces—the Scottish Government’s highly protected marine area proposal.
"The proposal is deeply controversial all over Scotland, and has even been compared with the second highland clearances.
"Is this not now the time for the UK Government to step in and work with the devolved," he said before being met with shouts of protest from the SNP benches.
"I will not be silenced," he continued, adding: "This matters deeply to my constituents. Deeply.
"Is it not time the UK government step in, work with the devolved administrations to come up with ... a conservation scheme that is acceptable in our fishing communities all round the UK?"
The Prime Minister Rishi Sunak, Conservative MP for Richmond (Yorks), replied: "The honourable gentleman makes an excellent point and is a passionate champion, as he should be, for his local fishing communities.
"He is right to highlight the concerns that have been raised not just by them but by members of the SNP about the potentially damaging impact of plans to introduce the highly protected marine areas in the way that they are.
"I would encourage the SNP Government to continue working with the Scottish fishing industry and coastal communities to understand their concerns. As we have seen them recently U-turn on other poorly thought-out decisions, hopefully they can re-look at this one, too."
A UK government pilot scheme for HPMAs is set to begin in July, with three zones in English waters to be given the special status.
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