One of the UK’s longest-standing funds for global nature protection is being drastically cut back, the Guardian has learned.

At least 89 countries will lose eligibility for funding for biodiversity projects under the Darwin Initiative, in a round of cuts that conservationists warned would put species and habitats in jeopardy, and set back global efforts to halt the precipitous decline in nature.

The Guardian understands that the regions to be dropped include most of Africa, central Asia and parts of Latin America. Countries such as Argentina, Iran, Sudan, Chad, Mali and Angola would lose out. Armenia, which is hosting the next conference under the UN convention on biodiversity this October, will also be excluded.

“At a time when governments have committed to CBD agreements to scale international biodiversity finance to $30 billion a year by 2030, continued cuts and restrictions risk undermining trust that those promises will actually be delivered,” said Andrew Terry, ZSL’s Director of Conservation and Policy. “For decades, the Darwin Initiative has been one of the UK’s most important programmes for supporting wildlife, improving livelihoods and tackling climate change in some of the regions that need support most. But reductions to the UK’s international aid budget and the removal of eligibility for 89 countries mean locally led organisations are losing vital backing at a time when communities and ecosystems are already under growing pressure. Projects funded by the Darwin Initiative are the frontline of efforts to protect communities from climate and ecosystem breakdown, and this is exactly the moment they should be strengthened, not scaled back.”

Catherine Weller, the director of policy at the conservation group Fauna & Flora, said: “We were shocked to see the extent of the geographies cast out of the Darwin Initiative this year – some good projects will now not be in contention. People living close to nature are its greatest champions, and Darwin is the type of funding they need.”

The Darwin Initiative was begun in 1992, announced by the Conservative prime minister John Major at the landmark Rio earth summit of that year, which produced the UN framework convention on climate change, the convention on biological diversity and the convention to combat desertification. Some of the initiative’s most high-profile projects have included reducing peatland tropical forest fires in Indonesia and helping to set up Bhutan’s first and only national botanical garden.

Some of the 89 countries to be excluded from eligibility are rapidly emerging economies or middle-income countries, whose status has changed markedly since 1992. These include China, India, Mexico and Turkey. Jenny Chapman, the international development minister, said earlier this year the UK would stop supporting G20 countries with international aid.

However, at least two G20 countries – Brazil and Indonesia – will still be eligible for Darwin funding, according to analysis seen by the Guardian of the next round of funding applications opened by the government.

It is not yet clear by how much the overall Darwin Initiative funding will be reduced, although the Guardian understand that existing funds will not be cut. News of the axe comes just a week after the UK hosted a big international aid conference, attended by more than 50 countries, at which climate and nature spending were celebrated.

The shrinking of the Darwin Initiative is likely to be the first of many cuts to nature projects this year. As the Guardian revealed earlier this year, as well as cutting climate finance to £2bn a year, from £11.6bn over five years under the previous settlement, ministers are ending the earmark within the climate finance target for at least £3bn to be spent on nature.

Last year, the Guardian revealed that a report by the UK’s spy chiefs had warned ministers that the collapse of vital ecosystems overseas, including the Amazon, represented a national security risk for the UK, as such collapses would raise food prices, incite migration and foment conflict.

Conservationists have been frustrated that the report, which was partly published in January, has not been acted on.

Adrian Gahan, of the Campaign for Nature, said the UK was reneging on vital commitments and harming its own national interests in the process. “The world struck a deal in 2022 that global south countries would protect their rainforests, wetlands and oceans, and donor countries would help them pay for it, because these places are vital infrastructure for all of us,” he said. “Expect far worse than 35C in Britain in May if we lose the Brazilian rainforest.”

Last week, the foreign secretary, Yvette Cooper, told an audience of ministers and high-ranking officials from scores of countries, and hundreds of aid professionals, that the UK was guided by “our sense of our shared humanity, that fundamental moral purpose to stand up against global disease and hunger, and to support those trapped in crises caused by conflict or climate change”.

However, many civil society organisations were frustrated at the emphasis that was put on bringing the private sector to bear on aid for the developing world.

A Defra spokesperson said: “We have made a deliberate choice to focus our efforts where biodiversity loss is most acute and where Darwin Initiative funding can deliver the biggest measurable difference for nature and people.

“The trade-off is clear: spread our efforts thinly or concentrate funding where it can achieve the greatest impact. The Darwin Initiative has been delivering for conservation and development across the globe for over 30 years and we remain committed to maximising its impact and achieving the greatest biodiversity benefit for all.”