Figures show there were 453 more deaths between October last year and this March, against the previous year, despite Scottish Government targets to cut mortality rates across the country.
Those working on the front line have cited the long winter, an increase in infections and an older population, including high numbers of people with chronic health condition, as contributing to the figures.
Just under 13,900 people died in Scotland within 30 days of admission to hospital during the cold season.
The figures were published along with the same data that sparked a high-profile investigation into raising death rates at hospitals in Lanarkshire.
A total of 13,890 people died in Scottish hospitals between October 2012 and March 2013.
This compares to 13,437 deaths for winter 2011-12, although this figure was down from the previous year when 13,828 deaths were recorded.
A campaign by The Herald has highlighted how hospitals are struggling to manage increasing numbers of elderly patients.
It was revealed this summer that ministers were warned 21 out of 24 accident and emergency departments in Scotland were regularly unsafe, months before the winter hospital crisis hit and hundreds of patients waited more than 12 hours for a hospital bed.
Full wards meant, in many cases, those arriving in A&E were kept on trolleys as hospital space filled up.
Alistair Douglas, president-elect of the Society For Acute Medicine, said hospital patients were generally now older and sicker than they would have been 10 years ago.
He added: "We all know last winter went on far longer than normal. It was not until early May we could feel things lift. Of course, the cold weather increases the case of respiratory tract infections, there are more infections in general and more people are in hospital for longer given that many will have continuing health conditions, such as heart disease or diabetes.
"Rather than be in hospital with, say, pneumonia for two to three days, they are in hospital for two to three weeks.
"If hospitals are full because patients are more ill, then it trickles down through the system and it is harder to find the capacity.
"In a sense, it is not a huge surprise if the number of deaths increases given that people in hospital are older, frailer and sicker."
A spokesman for the British Medical Association Scotland said boards needed to be able to work at a local level to adapt services when required.
Neil Findlay MSP, Scottish Labour health spokesman, said: "This week's barrage of health statistics reiterate the need for a full inquiry into the state of the NHS in Scotland, not least the increased number of hospital deaths over what was a mild winter.
"This was not a report card that reflected well on the Scottish Government's stewardship of the health service. The SNP needs to acknowledge that and act now to protect this valued institution and not just pass the buck on to hard-pressed staff who are working under intense pressure."
A Scottish Government spokesman said death rates typically varied during the winter.
He added: "That is why we use the Hospital Standardised Mortality Ratios, which are adjusted for these variables, and are a more accurate measure than simple mortality counts for helping us to improve patient safety and quality."