Thousands of environmentally important sites across England are coming under threat as the government body charged with their care struggles with understaffing, slashed budgets and an increasing workload.

Natural England has wide-ranging responsibilities protecting and monitoring sensitive sites, including sites of special scientific interest (SSSIs) and nature reserves, and advising on the environmental impact of new homes and other developments in the planning stages. Its work includes overseeing national parks, paying farmers to protect biodiversity, and areas of huge public concern such as air quality and marine plastic waste.

But these activities are being impaired by severe budget cuts and understaffing, Natural England employees and other interested parties have told the Guardian. “These are fantastically passionate staff who are worried that the environment is being affected so badly by these cuts,” one frontline staff member said. “There will be no turning back the clock” if we allow sensitive sites to be degraded.

The agency’s budget has been cut by more than half in the past decade, from £242m in 2009-10 to £100m for 2017-18. Staff numbers have been slashed from 2,500 to an estimated 1,500.

Conservation work on sites of special scientific interest is being cut, while farmers are finding it harder to access expert help on countryside stewardship. Work on areas such as air pollution and marine plastics has been cut and many nature reserves are being neglected as vital volunteers cannot be safely trained.

One 11-year veteran of the agency reported low morale and increasing difficulty in managing workloads, with sites left unmonitored for years. They said: “Our work brings economic benefits, environmental benefits, it helps communities. We have suffered disproportionately from the cuts to the Department for Environment, Food and Rural Affairs budget. It is such a shame as we have done some amazing and incredible work.”

The Prospect union has investigated the agency and concluded it is “at crisis point”, with staff overstretched and under stress after eight years of a 1% pay cap. The union will launch a report on Tuesday with a call on ministers to increase funding and remove the agency from the pay cap.

“Cuts have left Natural England at the point where its workers are saying they don’t have enough people or resources to do the things they need to do,” said Garry Graham, the deputy general secretary of Prospect. “If we are to be able to regulate our own environment properly after Brexit, it is vital that we cultivate and maintain the skills to do so domestically. We will no longer be able to rely on the EU to do bits of it for us. Once biodiversity is lost, it cannot easily be regained. Now is the time for the government to act.”

One senior manager told Prospect: “[Work on protected sites] is what many of us joined to work on and has been the central focus of much of our conservation work. There are currently no government targets for this work [so] cuts have fallen on work that is not protected, the largest area being SSSI work. That’s the stark reality.”

There have been widespread complaints from farmers over the agency’s failure to make timely payments for the countryside stewardship scheme, under which farmers undertake measures such as improving habitats for wildlife, wildflowers and pollinators. Payments have not been made on time, or fallen short, and many farmers complained of being unable to access the expert advice they need. This has discouraged farmers from applying to the scheme or continuing with it.

Guy Smith, the deputy president of the National Farmers’ Union, said: “We have thousands of members expecting payment from agri-environment schemes completely in the dark over when these already late payments will be made. It is imperative that Defra and its agencies give this priority.”

The Woodland Trust has called on Natural England to update a vital registry of trees, currently looked after by only one staff member. The registry helps campaigners to protect woodland resources that may be threatened by development and can help save money for developers at the planning stages. Updating it would cost about £1.5m over five years.

Abi Bunker, the trust’s director of conservation, said: “We recognise the pressures Natural England are under. It is frustrating when adequate progress cannot be made on updating the ancient woodland inventory, resulting in our rarest habitat being put at unnecessary risk.”

Caroline Lucas, the Green party MP who has asked a series of parliamentary questions on Natural England’s plight, said: “Behind the veil of Michael Gove’s fluffy rhetoric about caring for the environment, ministers have systematically gutted the agency that looks after irreplaceable habitats and beautiful landscapes. The result is plummeting morale as staff simply don’t have the resources to monitor thousands of protected sites across England, ultimately putting spaces for wildlife at risk of irreversible destruction.”

Tim Farron, the Liberal Democrats’ environment spokesman, said: “Farmers need certainty, the environment needs protection and Natural England needs a proper budget to do it. Instead Defra is failing in its duties.”

Defra’s budget has been one of those worst hit by austerity cuts. There has been a recent increase in staffing and funding but only to deal with the expected impact of Brexit on farmers and food supplies so those extra resources are unlikely to have a positive impact on Natural England’s work.

Marian Spain, the interim chief executive of Natural England, said: “Inevitably, cuts of almost 50% to the Natural England budget over the last five years have meant changes to the way we do things. Since taking on my role in December, meeting staff and hearing about the pressures they face has been one of my top priorities.”

A Defra spokesperson said: “The work of Natural England and its staff to protect our invaluable natural spaces, wildlife and environment is vital and its independence as an adviser is essential to this. As set out in the 25-year environment plan, Natural England will continue to have a central role in protecting and enhancing our environment for future generations.”