The proportion of NHS buildings classified as being in good condition rose to 70% last year.
The annual report looking at the NHS estate shows an improvement on the 58% recorded in 2014, and 66% in 2015.
There has also been a further reduction in backlog maintenance, falling by around 21% since 2011.
Backlog maintenance costs for 2016 were £887 million, down by around £11 million since 2015, or £45 million when inflation is taken into account.
The proportion of significant and high risk backlog maintenance has increased from 44% reported in 2015 to 47% reported in 2016.
This has largely been attributed to NHS Tayside, where the need for significant investment in Ninewells Hospital has been identified.
Health Secretary Shona Robison said: "This report finds that most NHS buildings are in good condition, and that boards are making steady progress in reducing the level of backlog maintenance across their estates.
"However, there needs to be sustained investment in facilities, equipment and vehicles to ensure that Scotland's health service can continue to provide a high standard of care.
"The Scottish Government has invested £1.8 billion in new assets and facilities over the last four years.
"This includes the new Dumfries and Galloway Royal Infirmary, due to open later this year, and the new Edinburgh Sick Children's Hospital.
"Additionally, over the next three years the NHS is planning to invest over £1.2 billion maintaining and improving the NHS estate."
Scottish Labour's health spokesman Anas Sarwar said: "It's disappointing to see that not only has the SNP Government failed to significantly reduce the building repair bill in our NHS over the last year, but more of the repairs carried out have been deemed high-risk or significant.
"The legacy of a decade of mismanagement and under-funding from the SNP, having to spend almost £1 billion on repairing buildings while our nurses suffer under a pay cap, is not what patients need."
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