The survey was carried out by the BMA, which represents doctors
Many hospital doctors are too scared to raise concerns about patient care or staff behaviour in case it affects their career, according to a survey.
The study by BMA Scotland found 40% of the 384 doctors questioned do not report issues of concern.
The organisation called for doctors to be given more protection from managers.
It said it had "concerns" about the culture within the NHS, and insisted doctors should not be afraid to blow the whistle.
Dr Charles Saunders, chairman of the BMA's Scottish Consultants Committee, said doctors had a "duty" to speak out when they are worried about hospital practices.
"However, as the results of this survey bear out, this is not always possible or effective", he added.
"We have concerns around the culture of many NHS organisations. Doctors tell us they fear their careers can be affected by speaking out - this is completely wrong.
"We must move to a culture where every individual in a health organisation can raise concerns that are looked at and acted upon appropriately."
Of the doctors who took part in the Standing up For Doctors; Speaking Out For Patients survey, some 80% were not aware of the whistle-blowing policy for employees at the NHS board under which they worked.
About six in every 10 doctors said they had experienced occasions when they have had important concerns about working practices or the behaviour of staff - but only 60% of those reported it.
Worries that reporting it would make no difference or fear of the consequences of doing so were raised as the doctors who said they did not raise concerns.
One in 10 doctors who did raise concerns said they were given indications that speaking out could have a negative impact on their employment.
Almost half of concerns - 44% - were over standards of care, while 37% were about the behaviour of fellow staff.
Around one in five cases related to targets or strategies of NHS boards.
"A culture-change needs to come from the very top," Dr Saunders said.
"Ministers and NHS board members need to send a clear message that they want to hear about things they can do better."
Boards will not tolerate harassment or victimisation of any member of staff who raises a concern
The BMA said it wanted the government and the NHS to do more to publicise health boards' whistle-blowing policies and to protect the right of doctors to speak out without risking their jobs.
A Scottish government spokeswoman said staff or patients should feel they can speak up about problems with the health service.
She said: "Every health board in the country has procedures to protect staff who raise concerns.
"Indeed, the Freedom of Speech policy that boards have to follow, states that boards will not tolerate harassment or victimisation of any member of staff who raises a concern and that includes informal pressure.
"Any example of that kind of behaviour would be treated as a serious disciplinary offence."
Scottish Labour's Jackie Baillie said: "It is important that anyone working in the NHS who has concerns about staff behaviour or patient care has the confidence to speak out.
"I would like to see the Health Secretary Nicola Sturgeon taking action to ensure that a culture of openness and transparency is encouraged and the views of staff are valued."
Scottish Liberal Democrat health spokesman Ross Finnie MSP said: "It is concerning that many health care professionals don't know how to blow the whistle.
"When a complaint is made it must be handled appropriately and must be brought to a conclusion."