The EU has passed a landmark law to protect nature after a knife-edge vote, ending a months-long deadlock among member states spooked by fierce protests from farmers.

But a last-minute change of heart by Austria’s Green climate minister, whose vote is credited with saving the proposal, led to fury in Vienna, with the party of the chancellor, Karl Nehammer, announcing it would seek criminal charges against her for alleged abuse of power.

“Today’s decision is a victory for nature,” wrote Leonore Gewessler on X after the vote on Monday. “My conscience tells me unmistakably [that] when the healthy and happy life of future generations is at stake, courageous decisions are needed.”

In an extraordinary display of division at the heart of Austria’s coalition government, Nehammer wrote to the Belgian presidency of the EU Council before the vote urging it to disregard his minister’s support and arguing that she did not have the right to take the position she had. Gewessler wrote in a separate letter that the chancellor’s allegations were “incorrect”.

The nature restoration law, which has proved to be the most controversial pillar of the European Green Deal and nearly failed at the final hurdle, sets a target to restore at least 20% of the EU’s land and sea by the end of the decade.

Lawmakers and governments had watered down the proposal in the months leading up to the European elections, in which far-right parties gained seats and green parties lost them. But despite concessions, supporters barely won over enough member states at the vote in Luxembourg on Monday.

“Today marks a significant day for Europe as we transition from merely protecting and conserving nature to actively restoring it,” said César Luena, a centre-left MEP from Spain who led the European parliament’s negotiations on the law.

The fraught proposal was nearly torpedoed in the European parliament last year and then pushed to the verge of collapse in March when Hungary unexpectedly withdrew its support. Ireland led a subsequent push to win over other countries, urging ministers to avoid backtracking on compromises that had already been agreed.

Until the final moments it was unclear whether supporters of the law had gathered enough votes to achieve a qualified majority of 55% of member states representing at least 65% of the EU population.

Environment ministers voted the law through with a wafer-thin majority after changes of heart by Slovakia and Austria cleared the bar by 1.07 percentage points.

Pieter de Pous, an analyst at the climate thinktank E3G, said: “No other part of the world has this little nature left, needed this law more and got so close to not having it.”

Austria’s support was key to tipping the scales. Gewessler had been a vocal advocate of the nature restoration law despite fierce opposition from her coalition partners. But until last month, her hands had been tied by a unanimous blockade from Austria’s federal states, which opposed the law.

That resistance appeared to crumble in recent weeks as two states – Vienna and Carinthia – announced they were satisfied with compromises made to the law, withdrawing their opposition without formally breaking the blockade.

Gewessler, who appears to be in a legal grey zone after her vote, announced on Sunday that she would back the law, having sought legal advice. “I cannot reconcile it with my conscience if we let this opportunity pass without having tried everything,” she said.

The public dispute has escalated to the highest levels of Austrian politics and threatens to tear apart the coalition government of the Greens, who control the environment ministry, and Nehammer’s centre-right ÖVP, who control the agriculture ministry.

Christian Stocker, the ÖVP’s general secretary, said on Monday that the party would file criminal charges against Gewessler for abuse of power. “The end does not justify the means: Leonore Gewessler is putting herself above the constitution because she cannot reconcile her green ideology with acting in accordance with the law.”

The final tally showed 20 countries voting in favour of the nature restoration law. Finland, Hungary, Italy, the Netherlands, Poland and Sweden voted against the law, while Belgium abstained. They criticised the cost of the proposal and said it would place too many administrative burdens on them.

Nature is dying faster than humans have ever observed and 81% of European habitats are in poor shape, according to the European Environment Agency. The EU lobbied other countries to commit to more ambitious goals to protect nature at a biodiversity summit in Montreal in 2022, but its leaders have since backtracked on national and European commitments.

“The EU needs to do its part to tackle the global biodiversity crisis,” said Magnus Heunicke, the Danish environment minister, during a debate before the vote on Monday. “Our citizens expect us to take decisive action and to do so without further delays.”

The law contains provisions to reverse the decline of pollinator populations such as bees by 2030. Member states will also have to put in place measures to restore drained peatlands and help plant at least 3bn more trees.

Copa and Cogeca, the EU’s biggest farming lobby group, criticised the slim majority of ministers voting in favour of the law, calling it a “flawed proposal” that would cause legal battles in regional, national and European courts.

“Political rhetoric aside, the question of the lack of clear and consistent funding for ecosystem restoration across the EU remains unanswered – partly explaining the great embarrassment and headlong rush that surrounds this law,” a spokesperson said.

Campaigners celebrated the vote as a “historic” win for Europe’s nature but criticised “persistent attacks” that had watered down the measures.

Špela Bandelj Ruiz, a Greenpeace biodiversity campaigner, said: “Despite the weakening of the law, this deal offers a ray of hope for Europe’s nature, future generations and the livelihoods of rural communities.”

A coalition of environmental groups led by WWF Europe called on member states to implement the legislation as soon as possible. “Today’s vote is a massive victory for Europe’s nature and citizens who have been long calling for immediate action to tackle nature’s alarming decline,” they said.