Some English hospitals are overspending by as much as £141m a year due to NHS underfunding, staff shortages and demand for care, according to Whitehall’s spending watchdog.

King’s College healthcare trust, which runs two hospitals in London, ended last year £141.4m in the red – the biggest deficit among England’s 232 trusts that provide services.

Ten trusts recorded a combined deficit of £758m in 2017-18, which was 69% of the £991m loss that trusts collectively posted, the National Audit Office (NAO) said.

Another London trust, Barts Health, had the second largest deficit – £108.8m – while the United Lincolnshire hospitals trust was £81.23m in the red.

In addition, the Department of Health and Social Care had to make £3.2bn of emergency loans to trusts in acute financial distress. This was an increase of £2.8bn on the previous year.

Growing numbers of clinical commissioning groups, the bodies that hold the NHS budgets in local areas, are also spending more than they receive. Together they overspent by £213m.

After eight years of tiny annual budget increases, the health service as a whole is carrying an underlying deficit of £4.3bn, the NAO said.

The figures show that the NHS in England is grappling with budgetary problems that are unsustainable, the NAO concluded in its annual review of health service finances.

The watchdog said it welcomed the government’s pledge to increase NHS funding by £20.5bn a year by 2023-24 after years of the service struggling to meet soaring demand while receiving tiny budget uplifts since 2010.

It warns, however, that a series of risks and conspicuously widespread understaffing threaten to undermine the NHS’s ability to deliver the ambitious plans to improve care set out in the long-term plan it published last week.

The NAO’s report stated that: “Difficulties in recruiting NHS staff presents a real risk that some of the extra £20.5bn will either not be used optimally – more expensive agency staff will need to be used to deliver additional services – or will go unspent as even if commissioners have the resources to commission additional activity, health care providers may not have the staff to deliver it.”

It also warns ministers that continuing to cut spending on public health, capital projects and medical education and training, in order to give the NHS more money for frontline care, “could affect the NHS’s ability to deliver the priorities of the long-term plan”.

Richard Murray, the chief executive of the King’s Fund, said hospitals were not to blame for overspending, even by sums as large as £141m.

Murray added: “Despite some NHS trusts being in the red by more than £100m, NHS Improvement aims to clear all provider deficits within two years. Complex NHS finances are bedevilled by short-term fixes, fragile workarounds and unrealistic expectations that leave some trusts in significant deficit whilst others are in significant surplus.”

Anita Charlesworth, the director of research and economics at the Health Foundation, said: “Workforce shortages are the greatest threat to delivering high-quality care to all those who need it. But spending on training and education has fallen by 17% in real terms over the last five years.”

A government spokesperson said: “The long-term plan, backed by a significant funding increase of £20.5bn a year by 2023-24, rightly sets out that putting the NHS back onto a sustainable financial path is a key priority and is essential to allowing the NHS to deliver further improvements in care.”

• This article was amended on 21 January 2019 to clarify in headline and first paragraph that the NAO figures reported in the story apply only to NHS England.