Earlier this year, the government produced its first comprehensive clean air strategy, the result of years of campaigning, public outcry and finally a series of court actions ending in victory for activist lawyers over resistant ministers.

For the first time, that strategy promised action on the key role that ammonia plays in the cycle of air pollution – previous pronouncements on air pollution concentrated on transport and industrial emissions.

The Bureau of Investigative Journalism and the Guardian has uncovered evidence on the state of ammonia emissions, the harm they do – 3,000 premature deaths a year could be prevented if they were halved, according to a leading researcher – along with the lack of regulation and monitoring, and the ineffectiveness of current efforts to reduce emissions.

Dealing with ammonia, as the evidence we have amassed shows clearly, is an urgent problem, but current schemes to help farmers reduce levels have been slammed as “inadequate” by the farmers themselves, making barely a dent in the rising emissions.

What’s more, the Guardian has found there is likely to be a sizeable gap, potentially of five to seven years, before a replacement system is operating. While the environment secretary, Michael Gove, has promised farmers “public money for providing public goods”, the environmental land management contracts that will provide that money are still unwritten and will only be phased in from 2024 to 2027. If nothing is done in between, those will be years of needless premature deaths, serious health problems and potentially irrevocable harm done to millions of children.

Vicki Hird, farming campaign coordinator at the group Sustain, said: “Air pollution is a hidden killer, for humans and wildlife, and increasing ammonia emissions from intensive farming need to be addressed urgently. Expecting farmers to act when they are facing a flood of cheap imports after Brexit, cuts to subsidies and a seven-year wait for an unknown farm support scheme is unreasonable.”

A spokesperson for the Department for Environment, Food and Rural Affairs told the Guardian: “Our clean air strategy sets out for the first time how we plan to tackle farm ammonia pollution by requiring and supporting farmers to invest in the infrastructure and equipment required to reduce emissions. We have already published guidance on how farmers can take action and will consult later this year on policy to reduce emissions from urea fertilisers, the first in a series of rules to reduce ammonia emissions from farming.”

Big reductions in ammonia can be achieved through simple measures. Covering slurry pits, tanks and lagoons stops it escaping to the air and good maintenance prevents it contaminating water supplies. Injecting slurry into the ground rather than spraying it over fields as a fertiliser makes a big difference. Growing trees and hedges can clean the air of some of the emissions before they can be carried away to mix with urban pollutants. And holding off fertilisers until the weather is right – not too hot, or wet – will cut down on the amount wasted.

“Farmers don’t want the nitrogen [from ammonia] going into the air. It’s no use to them there – they need it on the crops,” said Guy Smith, deputy president of the National Farmers’ Union. “Farmers are keen to improve their environmental performance.”

Facebook Twitter Pinterest Eutrophication in a river in Suffolk, predominantly caused by runoff from agricultural land. Photograph: geogphotos/Alamy

But many farmers, particularly small family farmers with razor-thin profit margins, reliant on taxpayer subsidies because of our demand for cheaper food, lack the resources to put even these measures into practice. One farmer contacted for the investigation spent £35,000, from a grant, on covering slurry storage – that could be the whole farm income for a year on many farms. Farmers are, on average, according to Defra, £227,500 in debt, with total farm debt standing at a record £19.3bn last September. And that is before Brexit ends the £3bn a year subsidies through the EU’s Common Agricultural Policy.

“Current assistance [from the government] is not adequate, and difficult to access,” said Smith. “We think there is a legitimate call for assistance from the government [to help farmers take the measures needed]. If there is regulation without the money being available, farmers may choose to quit farming and we will need to import more food from abroad, which may be cheaper but with lower standards and a higher environmental impact.”

Already, the costs of ammonia pollution are high: about £5bn a year for nitrogen and phosphorus pollution together, in damage to air and water quality, according to Tim Benton, dean of strategic research at Leeds University. “This isn’t just a farm issue, but a health issue,” adds Gareth Morgan, of the Soil Association.

Ammonia has been overlooked for many years, in part because vehicles and industry were the main focus of air pollution concerns, and also because it is not just a UK problem. The NFU’s Smith said some of the increase since 2013 has come from abroad, though that is impossible to verify without closer monitoring of UK sources, and Defra attributes the rise to manure and fertiliser use. Consumer habits play a role: our demand for meat, and for cheap food, means raising more livestock in intensive conditions, and a squeeze on farmers. If the government is to meet its promises on improving air quality, then changing farm practices – and providing farmers with the help they need to do so – as well as encouraging better diets, must be a core part of the future strategy.