The National Institute for Health and Care Excellence (Nice) has withdrawn long-awaited landmark guidance on ME hours before its planned publication amid a backlash from medical groups.

Charities and patient groups fighting for greater recognition of the poorly understood condition as a medical illness rather than a psychological problem had welcomed the planned guidance, which was due to stop advising doctors to administer a controversial therapy.

This disputed therapy, called graded exercise therapy (GET), involves incremental increases in physical activity to gradually build up tolerance. Patient groups have argued its use suggests those with ME have no underlying physical problem but are having symptoms due to inactivity.

Myalgic encephalomyelitis (ME), sometimes known as chronic fatigue syndrome, is thought to affect about 250,000 people in the UK and has been estimated to cost the economy billions of pounds annually. Characterised by pain and a long-term debilitating loss of energy, it affects one in four sufferers so severely that they are unable to leave the house and, frequently, their bed.

Other symptoms can include mental fogginess, light and noise sensitivities and trouble with memory and sleep. No specific treatment exists, although GET and cognitive behavioural therapy (CBT) have been used in an attempt to manage symptoms.

Nice last issued recommendations on ME in 2007. New final guidance, seen by the Guardian and roughly in line with a draft report published last November, would have abandoned the GET recommendation and also advised that CBT – a talking therapy commonly used to treat anxiety and depression – is not curative for ME.

Some scientists and medical groups have argued these two approaches are the only evidence-based treatments for the condition, but patient advocates have fiercely opposed this, in particular over GET, citing surveys that some patients have reported feeling worse after receiving the therapy.

Some critics within the scientific community have suggested that the clinical evidence base underlying GET for ME is of poor quality.

On Tuesday, leaks about the final Nice recommendations prompted angry reactions from some medical groups, which Nice suggested had triggered the pause in publishing. “It has become apparent that a number of professional groups are unwilling to support the guidelines,” a spokesperson said, adding that it was an unusual step and that a new publishing date had not yet been decided.

Charities and patient advocates voiced shock and disappointment. “Many medical professionals, researchers and patient representatives have spent three years diligently reviewing and assessing the evidence. The document has been approved by the committee and should be published,” the charities Forward ME, Action for ME, ME Association, Doctors for ME and ME Research UK said in a joint statement.

“The document removes support for therapies driven by outdated views regarding treatment for ME which are no longer supported by the science. We understand these new guidelines may take time to become accepted by elements of the medical community, but they should not be delayed.”

Sonya Chowdhury, of Action for ME, said: “We are in the dark about this. The Nice committee has worked hard to produce balanced guidelines which reflect science and best medical practice. Nobody should be able to undermine that.”

A spokesperson for the Royal College of Paediatrics and Child Health said it was “very pleased” about the pause and “we look forward to working with Nice to ensure that future guidance is of benefit to children, young people and those who manage their care”.

Dr Alastair Miller, a consultant physician in infectious disease and internal medicine and a former principal medical adviser for Action for ME, warned that “without CBT and GET, there is nothing” and added: “It is difficult to say where we go from here.”

Miller said: “The draft guidelines were predicted to stop the use of GET and limit the use of CBT which have served most chronic fatigue syndrome/ME clinicians and patients well for many years and were endorsed by the Nice guidelines in 2007. Most NHS clinicians use GET and CBT and have done so for a long time.

“Importantly, without CBT and GET, there is nothing. No new therapies or approaches have emerged since 2007, so in practice one needs to question whether there was ever a requirement to have a new guideline.

“If the professional bodies that represent those who care for these individuals were not prepared to support the guideline, this may have made Nice think again. It is difficult to say where we go from here. There are some amongst the charities and patient groups that are utterly opposed to CBT and GET, and so compromise and consensus may be difficult to achieve.”

The publication of the final guidelines had long been planned for this week, and the Guardian understands all stakeholders involved in the guidance were provided with an embargoed copy of the final report two weeks ago.