Eighteen health quangos will be reduced to between eight and 10 over the next four years. The fertility watchdog the Human Fertilisation and Embryology Authority (HFEA) and the Health Protection Agency (HPA), which deals with infectious diseases, are both slated to disappear in the shakeup.

The Health Secretary Andrew Lansley justifies the cuts on the grounds that it would produce savings of more than £180m over the next four years by streamlining the functions of these organisations and slashing their bureaucracy. Although the Department of Health's overall budget is being "ring-fenced", the ever expanding demands on the NHS each year mean that significant savings must be found.

Experts in infectious diseases criticised the plan to abolish the HPA as a statutory organisation and transfer its functions to the Department of Health and the new Public Health Service. "It's a very bad idea because the HPA is an absolutely essential national resource," said Hugh Pennington, emeritus professor of bacteriology at Aberdeen University. "There is no merit in making changes to the HPA other than those that strengthen it. It's quasi-independent and a degree of separation between it and the rest of government gives it more scientific freedom and independence," Professor Pennington said.

The HPA was central to advising the Government on the recent flu pandemic and has played an important role in monitoring HIV and Aids in the UK. It has also recently absorbed the functions of the National Radiological Protection Board, which was responsible for assessing the health risks of radioactive materials.

The fertility watchdog, the HFEA, was set up in 1991 to oversee the licensing of IVF clinics and lay down the guidelines for how this service should function. It was a model for other countries to adopt. But fertility clinics have complained of overzealous regulation and bureaucracy. Lord Winston, the fertility pioneer, criticised the authority in 2004 for incompetence and mismanagement, questioning why fertility medicine should receive special regulatory treatment.

Mr Lansley said yesterday that the HFEA will be retained for the time being but by the end of the current Parliament its functions will be divided between the Care Quality Commission and the Health and Social Care Information Centre, two of the health quangos to survive.

Lisa Jardine, the chair of the HFEA, said that IVF treatment still needs to be effectively regulated and that the authority's task is now to make sure this continues after the organisational change ordered by the Government.