Keith Brown has dismissed as "absurd" Fergus Ewing's description of the Greens as "hard left extremists" insisting the SNP's relationship in government with the party is "working very well".
Mr Ewing, a former SNP rural affairs secretary, has called for the pact with the Greens to end saying it was dragging down his party, while other senior party figures have called for the deal to go back to the drawing board.
Kate Forbes, the former finance secretary, has said it should be renegotiated while Alex Neil, a former cabinet minister, said members should have a vote on its future.
In the Herald on Sunday at the weekend, Mr Ewing said: "The SNP are tarnished, damaged and diminished by our continuing voluntary association with these hard left extremists - and unless the deal is scrapped this will only get far worse. Our polling support has dropped. The evidence is there for all to see."
READ MORE: John Curtice: Humza Yousaf to blame for SNP's slump in polls
Speaking to the BBC this morning Mr Brown, who is the SNP's depute leader, was asked about Mr Ewing's description of the Scottish Greens.
"That is an absurd characterisation of the Scottish Greens," he told BBC Radio Scotland Good Morning Scotland.
"We wouldn't as the SNP be in coalition with anyone described as extremists of any kind. I think it's been a very positive relationship. I worked in the government for a number of years we have our relationship which is pretty unique, which is very mature, which is very much in the mainstream practice in terms of coalition's so I support that process, I think it's working very well."
The Bute House Agreement was pursued by former first minister Nicola Sturgeon and marks its second anniversary later this month. It brought the Scottish Greens into government for the first time anywhere in the UK and in return Green MSPs must support ministers in any confidence votes and on the budget.
READ MORE: Ian Blackford: Bute House Agreement will continue to 2026
There have been tensions inside the SNP group at Holyrood over some policies - championed by the Greens - that are in the shared policy agenda which accompanies the agreement, including on gender recognition reforms and further restrictions on fishing. Both are currently shelved with legislation on the former being blocked by the UK Government and on the latter amid SNP backbench criticism.
Asked by the BBC if the SNP is "not a happy ship", Mr Brown said there is "no question" the party has "challenges".
He added: "That's probably no different from any other party at any given time."
Mr Brown also said he would support a debate on the Bute House Agreement between the SNP and Scottish Greens at his party's upcoming conference if a motion comes onto the final conference agenda, and adding that he still backs the deal.
He said: "If that's the case and people want to have that discussion, then if that gets on to the agenda then of course I would support that debate, but that is a process that has to be gone through.
READ MORE: Flynn rejects calls by ex SNP ministers for new vote on Greens' deal
"My own personal view is that we had a very comprehensive vote in favour of that Bute House Agreement and I remain very strongly in favour of that Bute House Agreement."
Some in the SNP have blamed the Greens for their party’s slump in the polls following a series of unpopular policies.
This has been rejected by Sir John Curtice, professor of politics at Strathclyde University, who said that the main fall in polling support coincided with the SNP’s leadership contest which ended in April with the election of Humza Yousaf.
Ian Blackford, the SNP’s former Westminster leader, said at the weekend that the party’s pact with the Scottish Greens “remains the right thing to do” and will remain in place until 2026.
During this morning's interview Mr Brown also revealed he has been subjected to abuse for his views on the gender recognition reforms passed by the Scottish Parliament last year.
He condemned personal abuse that has been directed at politicians throughout the debate surrounding the Gender Recognition Act.
He was asked about comments made by SNP deputy Westminster leader Mhairi Black at an Edinburgh Fringe show which compared "gender critical" activists to "white supremacists", but Mr Brown said he had not heard them.
He told the programme: "I have always tried to take a very straightforward approach and I'm not involved in abusing or calling anybody names in what I understand is a controversial issue.
"It was voted on by a vast majority of people in the Scottish Parliament and I stand by that vote.
READ MORE: SNP could end Yousaf leadership by giving new vote on Greens deal
"I do agree there should be no place for personal abuse. I have been subjected to abuse for my own views but I don't agree it's right to indulge in personal abuse.
People should have the right to have their say without having to suffer that kind of personal abuse."
Mr Brown was removed from his role as justice secretary in March in First Minister Humza Yousaf's Cabinet reshuffle. He had held Government positions since 2009.
Scottish Conservative Chairman Craig Hoy MSP, said: “Keith Brown’s cavalier dismissal of Fergus Ewing’s concerns about the Greens being in government with his party sums up how the SNP are fighting like Nats in a sack.
“The SNP’s deputy leader is clearly happy for the extremist and anti-growth Green tail to continue wagging the SNP dog rather than address any concerns over the Bute House Agreement.
“What is absurd is for Keith Brown to be saying the agreement with the Greens is working very well. He should try telling that to workers in the oil and gas industry who they would happily throw under a bus, or to communities desperate for road upgrades only to see the Greens put a stop to them.
“Like Humza Yousaf, Keith Brown appears to be in thrall of the extremist Greens despite the damage they are doing to Scotland.
“What is clear that he is very much on their side and others over gender recognition reform too when he shamefully sidestepped condemning the toxic rhetoric from his colleague Mhairi Black. That should have been simple for him to do, yet he typically deflected attention elsewhere.
“As the bitter infighting continues in the SNP, they are totally distracted from tackling Scotland’s real priorities. Only the Scottish Conservatives are focused on those real priorities such as tackling the cost-of-living crisis and reducing NHS waiting times.”
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