Environment Secretary Roseanna Cunningham has warned that the "UK's Brexit bandwagon" will make it harder for Scotland to fulfil its ambitions on climate change.
Being part of the European Union (EU) "makes it easier to take collective action to tackle these environmental challenges", the Holyrood minister said.
Ms Cunningham explained collective action with other nations across Europe was key in tackling issues such as climate change and also pointed to the role the EU plays in funding some of Scotland's top research institutions.
She told MSPs: "We simply cannot afford to take our chances by jumping on to the UK Brexit bandwagon and turning our back on the EU and all that a continuing relationship offers in terms of our environmental priorities."
Ms Cunningham said that Scotland, which brought in one of the first pieces of legislation setting targets to cut emissions, had "built up a reputation in Europe as leaders on climate change".
She stated: "Overall, we can be proud of our successes in seeking to protect our environment. The EU referendum result does not affect our commitment to build on these successes."
Scotland's position in tackling environmental issues is "much more aligned to the EU's position" than that of the UK Government, she added.
Ms Cunningham continued: "What the EU referendum result does do is create unnecessary uncertainty and, frankly, Brexit would make it more difficult to achieve our ambitions for the environment. So, we don't lose the ambition, it just gets made a lot harder to achieve."
She told how "world-leading research institutes in Scotland" have helped make "cutting-edge advances in agriculture, food and environmental research".
Ms Cunningham said: "Their research also helps inform policy decisions, both here in Scotland and in the EU.
"Indeed, the EU is also a major funder of these institutes, accounting for around £6 million in funding every year. The funding uncertainty is now considerable.
"The uncertainty is about more than just funding. EU nationals make up around one in six employees of the research institutes and their skills and experience are integral to their success."
Tory MSP Maurice Golden accused the SNP administration of "whingeing" and said rather than continually debating Brexit ministers should "focus on the powers which have been devolved and are fully in the competence of this Parliament".
He said: "This, overall, is the politics of grievance and the irony is that like a spoiled child the more powers that have been given to the Scottish Parliament, the louder the moaning and the whingeing gets from the SNP government."
Mr Golden accepted that "of course the EU has had a part to play" in efforts to tackle climate change, but said other international organisations like the United Nations and global treaties such as the 2015 Paris Agreement had also had a role.
He then suggested: "Of course, maybe the problem is the Scottish Government doesn't trust itself to look after the environment without intervention from the European Union."
Labour MSP David Stewart said: "The real threat from Brexit is that Europe's checks and balances may go. Who will enforce Brussels directives post-Brexit?"
Quoting from a briefing from Global Justice Now, he said: "The UK cannot go back to the sewage-ridden beaches and environmental destruction of decades past.
"It's of vital importance that any Brexit deal must involve the UK agreeing to fully maintain EU standards in areas like biodiversity, water and air quality."
Green MSP Mark Ruskell raised concerns about proposed trade deals such as the US-EU transatlantic trade and investment partnership (TTIP) and the Canada-EU comprehensive economic and trade agreement (CETA)
He said: "A post-Brexit bonfire of of environmental regulations, investment, research and subsidies from Westminster will only drive bad consequentials for budgets in Scotland and put our own green ambitions firmly back in the box.
"But the hard Brexit scenario offers an even more terrifying prospect of a race to the bottom in environmental and social standards, driven by neo-liberal trade deals that undermine the democratic will of citizens across the world.
"CETA and TTIP are not benign trade agreements that helpfully reduce tariffs and quotas.
"They allow public policy on everything from climate change to food standards to be challenged by corporations.
"The right to trade trumps everything and states that stand in the way can be sued through closed corporate courts."
Liberal Democrat Liam McArthur criticised the Scottish Government's "lack of progress" in reducing emissions in areas such as heat and transport.
He said: "There is nothing stopping the Cabinet Secretary taking a bolder, more ambitious path on the environment, whether inside or outside the EU.
"Yes, the current uncertainty over Brexit and the platitudinous mantra of Brexit means Brexit are wholly unhelpful, but it is not a justification for the Scottish Government to throw its hands in the air and say nothing can be done, or indeed for this parliament to renege on our responsibility to hold ministers to account on the environment."
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