Fergus Ewing has called for SNP members to be given another vote on the party's powersharing agreement at Holyrood.
The veteran MSP said that activists had backed the Bute House Agreement in 2021 without realising "the full enormity of dealing with these extremists."
His comments come after Robin Harper, the Greens’ first MSP, quit the party, attacking their position on independence and trans rights.
He said his former colleagues had “lost the plot” and that he will now vote for Labour at the next general election.
READ MORE: Robin Harper quits Scottish Greens, says party has 'lost the plot'
The Bute House Agreement brought the Greens into government and saw Patrick Harvie and Lorna Slater given ministerial positions.
In return, the SNP obtained a parliamentary majority to help them push through legislation and protect them from votes of no confidence.
The two parties agreed a joint policy platform covering a wide range of areas, including independence, housing, transport and tackling climate change.
It was backed by around 95% of SNP members.
Mr Ewing has long been critical of the deal, saying it gave the junior partners far too much power and influence.
He has previously dismissed the Greens as "wine bar revolutionaries."
The outspoken Inverness and Nairn MSP even risked losing the whip after he voted to sack Green minister Lorna Slater in a motion of no confidence over the failed Deposit Return Scheme (DRS).
Speaking to the Daily Mail, Mr Ewing said Mr Harper’s resignation should “send a message” to Humza Yousaf.
He said: “[Harper's] main charge, which is that his party has become a party of extremists, is spot on.
“The relationship that we had with the Green Party was supported, yes, by an overwhelming majority of our members in 2021, but that was before it was put into practice and before anyone realised the full enormity of dealing with these extremists.
“Perhaps now is the time to re-ballot SNP members.
“I suspect the result would be very different.”
READ MORE: Fergus Ewing says his Holyrood colleagues are 'not particularly happy'
A Scottish Greens spokesperson said: “The Bute House Agreement was supported by the vast majority of members from both the Scottish Greens and the SNP, as well as both MSP groups.
“The Agreement has allowed us to deliver real change for people and planet. Whether it is a £25 a week Scottish Child Payment that is lifting families out of poverty, free bus travel for everyone under 22 or a ban on new incineration and record investment in wildlife, nature and recycling.
"There will always be some who oppose change, they are entitled to. In the meantime, we will continue working in government to build a fairer, greener Scotland."
A poll published in April found that support for the deal among SNP members was at 53%, while 35% wanted it to end.
The agreement became a key battleground during the SNP leadership contest earlier with Mr Yousaf's rivals Kate Forbes and Ash Regan both critical.
In an interview with the BBC following his resignation, Mr Harper claimed Patrick Harvie and Lorna Slater had "forgotten about the centre of Scottish politics."
In a message to Green activist, Mr Harvie said his predecessor was arguing a position with “very little credibility”.
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