Andrew Lansley has been accused of lying about staffing levels in the NHS amid angry scenes at the Royal College of Nursing's annual congress.

The health secretary's claim that the number of clinical staff in the NHS has increased since the 2010 election was greeted with derision by many delegates, with some heckling or laughing and others shouting "liar".

The RCN has collected evidence, based on a variety of official sources, that 61,113 NHS posts across the UK have disappeared or been earmarked to be lost since it began monitoring workforce numbers a month before the May 2010 election.

Lansley insisted that although the number of nurses has fallen by almost 3,000 since the coalition took power, overall numbers of clinical staff have increased by almost 4,000, because of greater recruitment of doctors.

Despite care scandals linked to understaffing at hospitals such as Stafford, overall numbers of clinical staff were up across the NHS in England as a whole, he said.

"There are places across the country where from time to time the Care Quality Commission on our behalf, as the inspector, finds that staffing levels are not safe.

"Current warning notices are in place that staffing levels were thought not to be safe at Dewsbury, at Leeds, at Lancaster, at Mid Staffordshire, at Pembury and at Queen's hospital in Romford. That can happen and we do need to identify it," he conceded.

Lansley said NHS trusts were to blame for nurse numbers falling, not him. "Across the whole of the NHS we have seen staffing levels reduce. But clinical staffing levels overall have gone up by nearly 4,000. The number of qualified nurses has gone down by nearly 3,000 in two years in England but those are decisions made by trust boards," he said.

A succession of delegates intervened to say that Lansley's confidence about staffing levels did not match their own experience, with some raising concerns that falling numbers threatened patient safety and the quality of patient care.

Dr Peter Carter, the RCN's general secretary and chief executive, dismissed the health secretary's claim: "All this nonsense that there's more clinical staff than there was two years ago is just incorrect."

Delegates also derided Lansley's suggestion that any nurse worried care was at risk because of too few staff should raise their concerns with the management of their NHS trust. "If any of you have a view that staffing levels are literally not safe for patients I think part of your professional responsibility is to say that. Part of the responsibility of nursing directors and trust boards is to listen to what you are saying," he said.

Lansley, wearing an NHS lapel badge, was addressing the congress in Harrogate a year after delegates passed by 98% a vote of no confidence in him, at the height of the controversy over the health and social care bill. This year he made only a 12-minute speech and spent most of his hour-long appearance answering questions from delegates about key issues such as the NHS's financial squeeze, pensions reform, the potential closure of A&E and maternity units, and his desire to see more "market-facing" pay in the NHS, dependant on where staff worked rather than relying on national agreements.

Delegates loudly applauded nurses who took Lansley to task and claimed there was a gap – what Carter called a "disconnect" – between his insistence that the NHS is in good shape and the reality on the ground.

The health secretary reiterated the guarantee made last year that nurses would be granted a seat on the ruling boards of clinical commissioning groups – the local groups of GPs who will start commissioning and paying for care from April 2013. The NHS Future Forum recommended the move to soothe clinical opposition to Lansley's NHS reforms.

However, Carter said the pledge was not being kept and that he had written last week to Sir David Nicholson, the NHS chief executive, to outline his concerns about lack of representation.

Acknowledging the tension among nurses over Lansley's appearance, Carter said the absence of an "undignified spectacle" did not mean delegates believed the health secretary. "There's a great deal of unhappiness," Carter told Lansley, earning a standing ovation from the 1,200-strong audience.

The Department of Health said the total number of professionally qualified clinical staff in the NHS in England had risen by 3,600 (0.6%) in the two years between January 2010 and January 2012 – from 626,778 to 630,378. There was also an increase of 4,141 (0.7%) between May 2010 and January 2012, from 626,237 to 630,378, it added.

The department conceded that the total number of full-time equivalent qualified nurses, midwives and health visitors in England had fallen from 310,793 to 308,199 between May 2010 and January 2012 – a reduction of 2,595 (0.8%).

"The total headcount number of qualified nursing, midwifery and health visiting staff has decreased by 3,677 (1.0%) between May 2010 and January 2012, from 353,912 to 350,235," it added.

Ed Miliband will on Tuesday offer to join forces with Britain's nurses to fight the government's "reckless" reforms of the NHS, which he will depict as a betrayal of David Cameron's pre-election commitments.

The Labour leader is expected to receive a warm reception when he addresses the Royal College of Nursing Congress in Harrogate after Lansley's bumpy reception.

Miliband will announce that Labour is to launch a new service, NHS Check, that will allow patients and staff worried about the impact of the government's reforms to register their concerns with the party.