New guidance has been issued to doctors and nurses urging them to cut and delay doses of commonly prescribed antibiotics because of their role in the rise of hospital-acquired infections.

The initiative is an attempt by health officials to slash the use of antibiotics in hospitals by up to 25% each year, scrapping up to 83,000 routine prescriptions for conditions such as chest and gut infections.

Experts say the move will help the fight against the superbugs Clostridium difficile (C diff) and MRSA because although antibiotics kill some bugs, they cause others to spread.

Doctors and campaigners welcomed the plan, but critics warned individual patient care must not be compromised.

The guidance has been issued to health boards by the Scottish Antimicrobial Prescribing Group (SAPG), a panel of medicines experts, as part of the Scottish Government's drive against hospital-acquired infections.

The current culture of administering general antibiotics to many emergency admissions 'just in case' they respond to treatment will end. Instead, tests will be carried out to establish which, if any, antibiotics would be the most effective, delaying treatment by 24 hours.

Certain widely used antibiotics, cephalosporins and quinolones, believed to be particularly linked to the spread of C diff and MRSA, will be strictly rationed.

Antibiotics are implicated in the spread of superbugs because of they way in which bacteria respond to them. In the case of C diff, they kill 'good' bacteria in the gut that prevent C diff from growing and spreading. In the case of MRSA, the bacteria have grown resistant to certain types of antibiotic.

Professor Dilip Nathwani, chairman of the SAPG, said antibiotics "are being given for too long and the wrong ones are being given".

"Doctors and nurses need to think about whether patients need antibiotics and what the risks of antibiotics are."

Doctors would also be asked to keep duration of antibiotic courses to a minimum. "In most situations it can be three, five or seven days," Nathwani said.

"We are not being arrogant about it, we are going to measure and monitor this."

The move comes amid an alarming rise in cases of C diff, which causes diarrhoea and can be fatal. There were 1,861 cases in patients older than 65 in Scotland between January and March – a 16% increase on the previous three months.

In recent weeks an outbreak of C diff at the Vale of Leven Hospital in Alexandria, West Dunbartonshire, affected more than 50 patients, killing nine.

Official figures released last week showed that in 2006, 40 patients were killed by C diff in the area covered by NHS Lothian and a further 36 in Greater Glasgow and Clyde.

The C diff superbug has overtaken MRSA as the one most feared by patients. MRSA cases have dropped from 985 in 2005 to 881 last year.

GPs have already cut back on prescribing antibiotics for colds and flu.

Dr Charles Saunders, chairman of the British Medical Association's consultant committee and a public health doctor in Fife, said: "The risk benefits of antibiotics have changed over the years and now is the time to reassess how quickly you should use them.

"I think this will complicate things a bit for doctors, but it will improve patient care. It is likely they are going to have to do investigations and wait before prescribing.

"A lot of patients expect antibiotics and it can be difficult to explain to them why they are not getting them at that stage.

"But doctors aim to make patients better. In the long term this is an education for doctors and the public."

Derek Butler, chairman of the campaign group MRSA UK, said: "We would also like to see quicker tests that give results sooner so patients can be given the right antibiotics within a few hours, instead of waiting days. Obviously, other measures are also critical in tackling superbugs, including hand hygiene and cleanliness."

Families of patients affected by hospital superbugs have also welcomed the guidance.

Linda McCafferty, whose 82-year-old mother Nellie died after becoming infected with MRSA following a stay in Glasgow Royal Infirmary, said: "I support this move and I also believe patients should be swabbed for superbugs both on admission and on leaving hospitals."

However, Scottish Conservative health spokeswoman Mary Scanlon warned: "It is crucial that patients are monitored and that whatever happens is in the best interests of the individual patient."