Rishi Sunak has urged Holyrood ministers to reconsider the plan to introduce Highly Protected Marine Areas (HPMAs) to Scottish waters.
The Prime Minister was asked by a Highland MP to intervene to protect deeply-concerned constituents.
HPMAs, which would restrict fishing and other human activities, are designed to protect wildlife and the environment.
The Scottish Government has said they will not be imposed on communities which are "vehemently" opposed to them.
It has committed to designating at least 10% of Scotland's seas as HPMAs by 2026.
The BBC says a consultation on the scheme closed last month, with a further consultation on proposed sites likely to take place in 2025.
Fierce objections
Members of the Scottish fishing industry, coastal communities and even MSPs have raised fierce objections to the proposals.
Former finance secretary Kate Forbes warned people, not wildlife, could become the "endangered species" in Highland and island areas.
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.
At Prime Minister's Questions, Lib Dem MP Jamie Stone, who represents Caithness, Sutherland and Easter Ross, referenced the "astonishing sight" of former minister Fergus Ewing ripping up proposals for HPMAs in the Scottish Parliament.
Mr Stone told MPs: "This proposal is deeply controversial all over Scotland, and has even led to it being compared with a 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.
'Will not be silenced'
"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?"
Mr Sunak said Mr Stone had made an "excellent point", describing him as a "passionate champion" for fishing communities.
"And he's right to highlight the concerns that have been raised not just by them but by members of the SNP's own party about the potentially-damaging impact of their plans to introduce the Highly Protected Marine Areas in the way that they are," the prime minister said.
"I would encourage the SNP Government to continue working with the Scottish fishing industry and coastal communities to understand their concerns.
"And - as we've seen them recently U-turn on other poor-thought-out decisions - hopefully they can relook at this one too."
Bute House Areement
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.
Ministers propose that all forms of fishing, including recreational catch and release angling, would be prohibited in selected sites.
Seaweed harvesting would also be banned, no new marine renewable energy schemes would be allowed and the laying of subsea cables would be restricted.
Managed levels of swimming, snorkelling and windsurfing would be allowed.
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.
Ms McAllan has also vowed to meet with affected communities.
Take action
She said: "We must be prepared to take action that corresponds with the scale of the climate and nature crisis, but we must do so via a fair and just transition which empowers communities and shares in the benefits of a green economy."
The BBC says the controversy surrounding the issue sparked the first signs of backbench dissent since Mr Yousaf succeeded Nicola Sturgeon as SNP leader.
Former ministers Ms Forbes, Mr Ewing and Alasdair Allan all voted against a government motion supporting the proposals in a Holyrood debate last week.