The fight against Britain's biggest killer diseases could be hit by NHS plans to cut the number of dedicated teams of experts widely lauded for their work to improve care, doctors and health charities have warned.

Hundreds of specialists in cancer, heart disease and strokes face being made redundant as a result of the new NHS commissioning board's decision to shrink the number of clinical "networks" which are intended to drive up standards of treatment in hospital and help patients affected by those three conditions.

The board, the powerful new body that will take over running the NHS in England from next April, has decided to replace the 28 cancer networks and 28 combined heart and stroke networks with 12 of each. But the successor bodies will have far fewer staff and smaller budgets than the existing groupings of experts, which the NHS's medical director, Prof Sir Bruce Keogh, has praised as "an NHS success story".

The board said more patients would benefit because the new bodies would focus on a greater number of conditions.

The 700 staff working for the 56 networks may be cut to fewer than 100. Directors of the networks fear their slimmed-down replacements will be able to do far less to promote take-up of new forms of surgery and help patients throughout their treatment and recovery.

The rationalisation has prompted fears that it will affect patient care and set back the NHS's efforts to improve how it treats cancer, heart disease and strokes, which account for six in 10 of all deaths.

Prof Tony Rudd, the NHS's stroke director for London, said although the treatment of stroke patients had got better in the capital and Manchester, "there's a risk that future improvements in stroke care, which are still needed in many parts of the country, now won't happen".

"Heart and stroke networks will be severely reduced in size and number and therefore much less able to do some of the things they've been doing previously to improve care for the 100,000 people a year in England who have a stroke," Rudd added.

"I'm very concerned about the current plans. It would be a tragedy if we started losing things we have already gained. Heart and stroke networks do very important work. They have made a huge contribution to the NHS. But it's unclear what's going to happen to them. We are lobbying [the Department of Health and the NHS strategic health authority for London] hard to ensure that their expertise will be retained because there's a danger it won't be retained."

As things stand the three heart and stroke networks covering London's seven million-strong population are likely to be merged and there may be only a handful of specialists left driving up standards across the city under the new arrangements, he said. "There will be far fewer people than at present and less money for them."

Rudd feels the reorganisation puts at risk work to continue building on progress over the past decade, which has seen the number of people having a stroke and the death rate from strokes fall as well as victims' chances of recovering without having a major disability increase. The NHS's cash squeeze probably explains the board's decision, he said.

The British Heart Foundation is seeking "assurances that adequate funding will be provided [from April] and that cardiac specific expertise will be retained where needed".

Office for National Statistics figures show that heart conditions and strokes between them killed 158,084 people in England and Wales in 2010 while cancer claimed another 141,446 lives – 299,530 in all, or 60% of the 493,242 people who died that year. Across the UK, those conditions claimed 348,162 lives.

A survey of directors of 23 of the 28 cancer networks by Macmillan Cancer Support has revealed deep unease that key elements of their work may no longer be done from April. "The majority of network directors expressed concerns about the impact of the structure change on their ability to deliver their functions in the reformed NHS," it found.

Several directors described networks as "the glue" that provides "stability and knowledge" to GPs, hospitals and charities involved in efforts to improve treatment of disease. Others fear that downsizing cancer networks could result in services undergoing "fragmentation" or "disintegration", hit efforts to improve patients' experience of NHS cancer care and mean relationships of trust built up over years disappear because fewer staff will be covering a much bigger area.

John Baron, the Conservative MP who chairs the all-party parliamentary group on cancer, said: "Cancer networks provide a valuable service to patients. Their expertise provides support where necessary. This allows clinicians to spend more of their time on what is most important – their patient. It is essential that this expertise is retained within the NHS, yet we risk losing it."

The Cancer Campaigning Group, which represents 40 cancer charities, said shrinking cancer networks could deprive the new GP-led clinical commissioning groups of key insights. "Research we have undertaken showed that 82% of GPs with a responsibility for commissioning will need specialist advice. Plans to move away from specialist support teams would severely limit the ability of cancer networks to provide the vital knowledge commissioners need and we urge the government to reconsider these proposals."

The commissioning board plans to spend £42m to create 12 "network support areas". Each will manage new "strategic clinical networks" in their regions, which will cover four, instead of the existing two major types of healthcare: cancer; cardiovascular disease; maternity and children; and mental health, dementia and neurological conditions. There is likely to be one network in each of the 12 regions covering each of these four areas of care.

A board spokeswoman said: "These arrangements represent an increase in the range of conditions/patient groups that will benefit from nationally supported clinical networks [which] have the potential to make huge improvements in the way care is managed in the NHS."