A total of 55% of workers questioned agreed that care of patients was the top priority of the health board they worked for. Based on responses from nurses and midwives, the figure dropped to 45%. The 55% figure was down 8% on last time.
The snapshot also found only one-third believe there are enough staff for individuals to do their job properly - although this was up 3% from the last time the survey was done three years ago.
In other findings, just less than two-thirds (62%) of workers did not feel they had a choice in deciding what they do at work and only one-quarter (26%) felt they were always consulted about changes.
But the new survey, released by the Scottish Government, paints a mixed picture of job satisfaction.
There are some positive findings, including the majority of staff (87%) saying they are still happy to go the "extra mile" when required.
For the first time more than half of workers - 52% - say they feel confident about speaking up and challenging the way things are done. However, only 31% believe there are enough staff to allow them to do their job properly. This dropped to just 24% based on responses from nurses and midwives.
And while three-quarters of staff say they still plan to be working for their health board a year from now, only half of employees would recommend it to others as a place to work.
A total of 44,389 NHS Scotland employees completed the questionnaire, 28% of the overall workforce.
The statistics come just a week after a survey by nurses organisation RCN Scotland found that half of nurses felt under too much pressure to give the best care to patients. Director Theresa Fyffe said: "The fact that less than half of our nurses and midwives feel boards have care of patients as their top priority is a damning indictment of the Government's stated aim to make NHS a world class, patient centred organisation.
"The results of the NHS staff survey and our own employment survey paint a picture of an NHS where nursing and midwifery staff are trying to do their best and deliver high-quality care for their patients, yet the systems, attitudes and the daily pressures are all stacked against them."
However, the survey also highlighted low levels of bullying and harassment at work. Almost nine in 10 employees (89%) said they were not being bullied or harassed by their manager, and 85% said they were not experiencing bullying or harassment from colleagues.
Among those who said they did feel victimised at work, 36% had reported it to bosses - a slight increase on 2010. However, the majority of those who had not reported it said this was because they thought nothing would be done or they feared negative consequences.
Dr Brian Keighley, chairman of the BMA in Scotland, said: "It is extremely disappointing that the survey illustrates the lack of confidence that NHS staff have in speaking out against bullying, discrimination or cases of violence or aggression.
"A shift to a more positive culture, where NHS staff can raise concerns and feel that they will be listened to, without fear of recrimination, must be a priority for the Scottish Government and NHS boards."
Michael Matheson, Minister for Public Health, said: "There can be no doubt our staff are the heart of our NHS. The many achievements of our NHS are down to them and the dedication they show to patient care.
"As a result, we want every member of staff to know we will do everything we can to ensure they feel supported to do their job.
"The staff survey results have given us important feedback on areas of progress, but, more importantly, where we need to focus our attention to make necessary improvements."