An official warning system highlighted higher death rates at the Vale of Leven Hospital in Alexandria and the Royal Alexandra Hospital (RAH) in Paisley - whose figures were combined - as well as the Western Isles Hospital and Caithness General Hospital.
Hospital Standardised Mortality Ratios (HSMR) examine average death rates, based on hospital size and other factors, which are then compared to numbers of actual deaths.
Overall death rates have fallen by 7 per cent since January to March 2014 however Caithness General Hospital had nearly double the predicted death numbers in April to June this year.
Western Isles Hospital, the RAH and the Vale of Leven were also flagged up.
NHS Highland said the figures were incomplete so it could not draw any clinical conclusions.
The Scottish average HSMR was 0.86, with 5,861 deaths compared to the 6,782 predicted, with better treatments and changes to end of life care cited as possible explanations for the downwards trend.
Health Secretary Shona Robison said the reduction was testament to the success of the pioneering Scottish Patient Safety Programme, which was introduced in 2008 to drive down mortality rates.
Eight hospitals saw a significant decline in death rates, including Ayr Hospital where mortality rates plummeted by 15.6 per cent.
Raigmore Hospital in Inverness and Queen Elizabeth University Hospital in Glasgow had HSMRs well below the national average, at 0.58 and 0.77 respectively.
Ms Robison said: “These latest figures show that, since the first quarter of 2014, there have been 7 per cent fewer than expected deaths in Scotland’s hospitals – a testament to the efforts of our NHS staff working every day to reduce harm and improve safety for patients.
“Today’s mortality statistics show exactly why our Scottish Patient Safety Programme deserves its international reputation as a world leader and the numerous copies of it around the world.
“It is particularly encouraging to see that our newest hospital, the Queen Elizabeth University Hospital, has a hospital mortality rate that is significantly below the national average – showing the benefits of delivering the most modern models of care in the most up-to-date healthcare facilities.”