NHS Quality Improvement Scotland (NHS QIS) said the problem of Hospital Acquired Infections (HAIs) affects more than 33,000 patients every year and costs the NHS millions of pounds.
In its first report, the watchdog said a "culture of surveillance and vigilance" must be introduced to tackle the problem.
Responding to the report, Health Minister Malcolm Chisholm said NHS trusts and boards must "actively manage" infection control to cut the risks.
HAI has been a key factor in about 457 deaths a year and a contributory factor in a further 1,372.
The report said these infections cost the NHS an estimated £186m a year while about 380,000 bed days have been lost due to delayed discharges, ward closures and surgery closures.
NHS QIS said management must give infection control measures a higher priority, with improved co-ordination of activity, more staff support and increased monitoring of procedures.
There were examples of "good practice" but it stressed that every NHS worker must take responsibility for HAIs.
Training programme
The report said: "The real challenge for NHS Scotland is to introduce a culture of surveillance and vigilance.
"Standards that have been validated and evidenced in this report provide a sound starting point.
"Our recommendations, if implemented, will go a long way towards establishing efficient infection control systems in all trusts."
The report added that infection control must be an issue for health professionals, staff, managers, patients and their families.
Mr Chisholm said the report would build on the work already done by the Scottish Executive in the fight against HAIs.
Last year, the minister announced a series of measures including an infection control training programme for nurses, increasing the number of infection control nurses and the setting up of a new monitoring unit.
Mr Chisholm said: "The key to tackling HAI is better infection control in our hospitals.
"Healthcare professionals cannot eliminate all infections, but this report is telling us that more can be done to manage and reduce avoidable infection."
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The best way to tackle these health risks is by bringing in Modern Matrons or Super Sisters
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Mary Scanlon MSP, Scottish Tories
However, Scottish National Party deputy health spokeswoman, Shona Robison MSP, attacked the executive's record on the matter.
She said: "Until we see the end of the privatisation of hospital cleaning services and the Scottish Executive stop putting profits before patients this problem will not be overcome.
"Patients should enter hospital to be treated not infected and the Scottish Executive must accept that patient safety should be paramount."
Scottish Tory health spokeswoman, Mary Scanlon MSP, said: "The best way to tackle these health risks is by bringing in Modern Matrons or Super Sisters who will supervise wards and ensure they are kept free from dirt and risks of further illness.
"It's estimated HAIs drain the NHS of £186m every year, I'm sure I am not alone in saying this money could be used to prevent the problem."