The first minister and health secretary have apologised to patients who have faced delays for treatment as a result of winter strain on the health service.
Nicola Sturgeon said NHS Scotland was facing “exceptional” pressures but coping despite difficult circumstances.
Latest figures showed the number of people suffering from flu has more than doubled compared with last year.
Health Secretary Shona Robison said she would examine if more could be done to encourage the uptake of the vaccine.
Opposition parties criticised the Scottish government saying these challenging pressure were not unforeseen.
Speaking during a visit to Perth Royal Infirmary’s A&E department, Ms Robison told BBC Scotland: “Where there is a concern is for those who are under 65 with an underlying health condition.
“We want more of those people to go and get vaccinated because we know the impact of flu on them can be very, very severe indeed.”
About half of NHS boards across Scotland have reported significant ward pressure as a result of dealing with people suffering from flu.
Speaking on the BBC’s Good Morning Scotland radio programme, Ms Sturgeon said: “I would apologise unreservedly not just during the winter but at any time of the year to any patient who is not seen as quickly as we would want them to be seen in the NHS or who doesn’t get the treatment that they have a right to expect.
“We have seen exceptional pressures this winter largely due to the increase in flu cases but also, particularly in the period immediately before Christmas, weather-related pressures, but the hard work, the incredible hard work, the incredible teamwork, of the staff of the NHS – and I want to take this opportunity to thank each and every one of them – means that our NHS is coping in very, very difficult circumstances.”
Provisional figures suggested uptake of the flu vaccine was similar to last winter.
Ms Sturgeon said early information suggested rates had increased slightly among NHS staff, with less than 50% vaccinated last year.
The Scottish Conservatives have argued ministers should have done more to boost uptake.
During her visit to Perth Royal Infirmary, the health secretary praised the efforts of NHS staff over the festive period and apologised to patients who had to wait for treatment.
“Any patient waiting longer than they should to be seen and treated within the NHS, I would apologise for that,” said Ms Robison.
“But I think the public understand that we are in exceptional circumstances here and I have had lots of messages from the public saying staff, in the face of huge pressures and challenges, have done a tremendous job.”
Responding to concerns over flu vaccine uptake, she said: “There was a really robust, big campaign to promote vaccination, in the same way as we have done in previous years, not just for the public but health and social care staff as well.
“We can’t force people to get the vaccination, all we can do is promote and encourage, and we used every communication channel possible to get that message across.”
The health minister added that winter pressures were expected to be reflected again in A&E waiting-time figures.
The number of patients seen within the target four-hour waiting time was well below the 95% target in the weeks before Christmas.
Weekly statistics, due to be published on Tuesday, will cover the period between Christmas and New Year.
Ms Robison said: “The A&E figures will remain very challenging indeed and people are working very, very hard to keep patients safe and, of course, people within A&E will be seen and treated and discharged as quickly as possible.
“The week was one of the most challenging weeks.
“Of course our A&E performance prior to that has been the best in the UK for over two years, so A&E performance was very, very strong, but it has been impacted by these winter pressures and that will remain the case for the short-term while they get into recovery mode.”
Conservative health spokesman Miles Briggs said Scotland was failing to meet the target of having half of all NHS workers vaccinated against the flu while in England almost two-thirds (63%) were vaccinated.
He added: “The impact of this is devastating – it means doctors and nurses unable to come into work and patients suffering further delays as a result.”
Labour health spokesman Anas Sarwar said an apology from the First Minister “just isn’t good enough for patients and NHS staff failed by the SNP government this winter”.
He said: “These were not unforeseen circumstances. Our NHS faced a similar crisis last winter yet the SNP overtly failed to make the preparations necessary to avoid another winter meltdown.”