Healthcare Environment Inspectorate (HEI) chief inspector Susan Brimelow said the spot checks were paying dividends as the latest annual report showed wards and equipment were generally cleaner.
The report by the HEI said the number of failings and shortcomings found by inspectors during announced and un-announced visits to hospitals had fallen to their lowest rate since the regime began.
The number of "requirements" issued between October 2011 and September 2012 had fallen to 110, compared to 172 in 2009/10, equivalent to a rate of 3.5 per inspection.
Requirements refer to improvements ordered by inspectors to ensure a particular ward or facility meets the national standards for controlling healthcare associated infections, laid out by NHS Quality Improvement Scotland.
Inspectors were also handing out fewer recommendations – best practice guidance which the HEI believes hospitals should follow to improve standards of care.
There were 81 recommendations issued in 2011/12, compared to 180 in 2009/10, equivalent to a rate of 2.6 per inspection.
The report refers to 31 inspections – 25 unannounced and six announced – carried out at 31 acute hospitals and services in 14 health boards.
By looking at the findings, the HEI aims to build up a picture of the quality of infection control, hygiene and cleanliness in hospitals across Scotland.
The inspectorate was established in April 2009 in the wake of the fatal clostridium difficile outbreak at the Vale of Leven Hospital in Alexandria, West Dunbartonshire.
It was commissioned to undertake at least one announced and one un-announced inspection to each acute hospital in NHS Scotland every three years.
Yesterday's annual report was the first since unannounced inspections were rolled out in June last year, a move Ms Brimelow has credited with driving up standards.
She said: "It is encouraging we are seeing evidence of real improvements including generally cleaner wards and patient equipment.
"This improvement is reflected in the reduced number of requirements and recommendations we have had to make, and this is particularly pleasing given the vast majority of our inspections were unannounced.
"Nevertheless, there is no room for complacency as we continue to identify key areas for improvement.
"I am confident our programme of predominantly unannounced inspections is paying dividends and we will continue to scrutinise hospitals in this way, working with NHS boards to focus on those areas that still need to improve.
"I feel cautiously optimistic we are seeing progress but NHS boards must not take their eye off the ball and should always be ready for inspection."
The improvement coincided with a fall in the incidence of hospital superbugs over the same period.
Cases of C.diff among patients over-65 fell 37% in 2011/12 compared to 2009/10, while cases of MRSA had fallen by 35%.
The report was welcomed by Health Secretary Alex Neil as he officially opened the Royal Victoria Building in Edinburgh.
The £43.6 million facility, on the Western General Hospital site, comprises 147 single rooms, each with its own ensuite shower and toilet facilities.
Mr Neil said: "I am encouraged to see notable improvements in hospitals, but we are not com-placent and I recognise there are still a number of areas where further improvement is needed.
"All boards have been left in no doubt they must act now to tackle any issues raised in these reports as a matter of urgency."