The comments came as the Scottish Conservatives said they would vote against the appointment of co-leaders Lorna Slater and Patrick Harvie to government minister posts.
Speaking on BBC Radio Scotland’s the Sunday Show, the soon-to-be government minister responded to criticism from the former BBC journalist that Mr Harvie’s party is full of “eco-zealot Marxists”.
Asked whether there was a risk the Scottish Greens may become a shield for criticism used by Nicola Sturgeon to avoid blame by joining the cooperation deal with the SNP, the co-leader took aim at “far right newspapers”.
Admitting there was risk to his party, he said: “There’s a risk for both sides in this and neither side needs to do this.
He added: “If you look at the slightly more raving coverage in the far right newspapers and certain former colleague of the BBC, very right wing pundit now, Andrew Neil, I mean really extraordinary, extreme, hard-right reactions.
"Now the SNP did not need to expose themselves to that by working with us, they know that there are certain forces that regard anything to do with green politics as some kind of communist conspiracy.
"Both sides are taking a risk, I think we are taking a risk because we are convinced that by working together, we can do better for Scotland.”
Mr Harvie was also asked whether it was a decision by the Scottish Greens or by the SNP to turn down full cabinet secretary jobs as part of the cooperation deal.
The Green politician said that due to the deal falling short of a full coalition and a reticence to be bound by full collective responsibility, the decision had been made to take junior minister roles instead.
He said: “It’s a little bit more nuanced than a coalition and it does mean that we didn’t feel that could take complete collective cabinet responsibility.
"And I think it would be reasonable from the government’s point of view that anyone who is a full member of the cabinet is fully signed up to collective responsibility.”
He added: "We’ve always been far more focused on what is the government going to do differently as a result of this cooperation agreement, rather that whose name is on which ministerial door.
"But as it became clear that there really wasn’t scope for a full coalition because we had significant differences on a number of issues, we weren’t willing to accept the idea of complete collective responsibility, I think it would be appropriate not take full cabinet positions.”
Both Ms Slater and Mr Harvie will be approved as ministers in Holyrood this week, but will face opposition from the Scottish Conservatives.
Stephen Kerr, the party’s chief whip, said the Tories would oppose the move and the “coalition” as it would weaken the Scottish Parliament if the Greens retained privileges given to opposition parties.
He said: “We cannot accept the Greens’ ludicrous attempt to game the system by being in government and opposition at the same time. This nationalist deal is a coalition, according to the Greens’ own constitution. It will see the Greens join the government and be bound by agreement to support the SNP in votes.
“The Greens cannot have their cake and eat it. The Scottish Parliament will be weakened if they are allowed to hold government office and retain the rights of opposition parties, including receiving additional funds and a key position at First Minister’s Questions."
Labelling the Scottish Greens as "extremist”, Mr Kerr said the party was a “danger” to Scotland.
He said: “As we deliver our recovery, we also cannot endorse extreme Scottish Government ministers who would recklessly risk jobs and businesses. Patrick Harvie and Lorna Slater freely admit that they want to hold back our economy. They have said themselves they are against “endless economic growth”.
“The extremist Greens are not fit for office. They’re a danger to Scotland’s economic recovery with their anti-jobs, anti-business ideological agenda. Only the Scottish Conservatives will stand up to the serious economic threat posed by this nationalist coalition of chaos.”