The Rainbow Greens, the party’s LGBT wing, has also criticised the announcement, which came on the same day that the prescription of puberty blockers for new patients under the age of 18, at the gender identity service in Glasgow, would be paused.
The decision followed a landmark review of gender services for under-18s in England and Wales.
Scottish Greens co-leader Patrick Harvie said he would be urging members to back the powersharing agreement so the party could “put Green values into practice” in government.
Writing on X, he said “many” members had been calling for an EGM to discuss the future of the agreement.
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But Mr Harvie said: “As part of the Scottish government, we’re making a difference on a far bigger scale than ever before.”
It comes less than three years after the Bute House agreement brought Greens into government for the first time anywhere in the UK, in August 2021.
The deal, named after the first minister’s official residence in Edinburgh, crucially gave the SNPa majority in the Scottish parliament when its votes there were combined with those of the seven Green MSPs.
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The agreement gave ministerial posts to the Scottish Green Party’s co-leaders Mr Harvie and Lorna Slater.
On calling a vote, Ms Slater said: “The intention, as a democratic party, is to give members the opportunity to debate and decide how the party moves forward.”
Ms Slater added: “Not everything in politics is easy, as we have seen over recent years, months and days, but our strength as a green movement is in standing up against those destructive forces who would set fire to everything we have achieved if given half the chance.”