The report said that, while there had been a general improvement in hospital cleanliness, progress is undermined by basic failings in relation to patient equipment.
This relates to beds, mattresses and commodes - as well as management of needles, waste and linen and continuing concerns around hand-cleaning by NHS staff.
The latest report by the Healthcare Environment Inspectorate (HEI) said wards were cleaner, staff knew about their role in infection control, and inappropriate prescribing of antibiotics had been curbed.
In the four years since the HEI was established there has been a strong decline in both serious breaches and more general criticism, against a backdrop of an increasingly tough regime in which inspections have become unannounced.
Susan Brimelow, chief inspector of HEI, said: "Overall, the public should be assured by our findings which show that NHS Scotland continues to make good progress in raising standards of hospital cleanliness, hygiene and infection control.
"NHS boards are clearly taking our inspections seriously and when we do raise concerns with NHS boards we see from their action plans and our own follow-up inspections that this results in clear action to raise standards.
"However, it is vital that improvements are not just made as a short-term action following our inspections - they need to be sustained over time."
She said that, in spite of the general improvement, it was particularly disappointing to find recurring areas where improvement was needed.
She said: "For example, too often inspectors find that patient equipment is not clean. Good examples exist in other healthcare systems where dedicated patient equipment teams and equipment stores ensure patient equipment is clean and ready for use.
"We will continue to work with every NHS board to continue to raise the bar and ensure that, together, we provide a safe and clean environment for patients at all times, and the awareness of snap inspections."
The facts and figures of the inspectorate's four years in operation suggest broad improvement, with serious issues raised being 172 in year one and 210 in year two, but falling dramatically to 110 in year three. The most recent year, 2012-13, saw a further fall to 104 but with more unannounced inspections, which it was felt made the overall picture more encouraging.
Stated highlights in the report were:
l Hospitals inspected by HEI were generally clean and well maintained.
l NHS staff were clear on their roles and responsibilities in relation to infection prevention and control.
l Good compliance in relation to the prescribing of antibiotics.
Ms Brimelow said improvements were welcome but that there was no need for some of the adverse findings, such as poor cleanliness of bedframes and mattresses. However, she denied the problems were caused by restrictions on NHS budgets.
She said: "I don't think this is anything to do with funding. These are basic standards which I think patients should expect.
"This isn't hard to deal with and every patient should expect a clean bed when they arrive in hospital. That is why we need to look nationally at other systems."
Health Secretary Alex Neil said: "NHS Scotland has a robust scrutiny regime in place and I am confident that this system is continuing to drive improvement. It is encouraging that we are continuing to make good progress in raising standards of cleanliness in hospitals.
"However, I share the Inspectorate's disappointment that there are recurring areas where improvement is still required."