Alison Johnstone has confirmed the Scottish Greens will no longer have a weekly question at FMQs and said she hoped members would agree with the changes and “recognise” it was fair for all parties.
The Scottish Greens’ co-leaders Patrick Harvie and Lorna Slater were approved as ministers by MSPs on Tuesday.
But under fresh details released on Tuesday, it was confirmed the Greens would no longer have the right to respond to ministerial statements, and would have their allocation of "short money" funds cut.
Criticising the agreement, newly-elected Liberal Democrats leader Alex Cole-Hamilton said said: “We need to fight the climate emergency with ferocity, but without the baggage of nationalism.
"The planet doesn’t have time for the new nationalist coalition to drag us back to the all-consuming divisive constitutional arguments of the past.
"This is thin gruel for the Green Party."
Scottish Labour leader Anas Sarwar also criticised the agreement, saying it was “about how the government looks, not how it can deliver for the Scottish people”.
He said: “This is merely the confirmation of a long-standing coalition of cuts and will lead to the cost to the taxpayer of the Cabinet ballooning.
“This is not a clean start – this is about the constitution, not the climate, about control, not co-operation.
“The people of Scotland and future generations deserve so much better than this.”
The co-operation agreement, which has now been endorsed by both parties, will see the Greens form part of the government for the first time anywhere in the UK.
The Presiding Officer explained the decision to take away a leader’s question at FMQs, writing: “However, the scope of the agreement (and accompanying shared policy programme) together with the ‘no surprises’ approach to matters of parliamentary business, establishes a different relationship between the Scottish Government and Green Group than exists between any other parties and the position of the Scottish Greens as the third largest opposition party in the Parliament is fundamentally altered.
“The agreement therefore requires a bespoke response here at Holyrood, one which draws on precedents and practices, is fair to all parties represented in the Parliament, and is commensurate with the requirements of robust parliamentary scrutiny.
“In my view, the nature of the co-operation agreement, which would see the two Greens co-leaders being appointed as junior Scottish ministers, removes their entitlement to a leader’s question at FMQs.”
The Scottish Greens will lose their slot at the opening and closing of speaking during a debate, and will now get a speaking slot in the same way as the Liberal Democrats.
The Scottish Tories welcomed the decision.
Party chief whip Stephen Kerr said: “The Scottish Conservatives had strongly opposed the Greens’ attempts to have their cake and eat it.
“We rejected their efforts to game the system, as they sought to join the government and somehow pretend to still be an opposition party.
“We welcome this firm, but fair decision from the Presiding Officer, which removes the Greens from their leader’s position at First Minister’s Questions … the Greens had tried to undermine the Scottish Parliament, but the Presiding Officer has made sure that will not happen.”