Survey results reveal around a quarter of nurses (24%) say they have been discouraged or warned off raising certain issues.
More than 8,000 RCN members responded to the survey with almost half (44%) saying worries about victimisation or reprisals would make them think twice about whistleblowing.
Health minister Dan Poulter said NHS staff who speak out in the interests of patient safety must be "protected and listened to".
Peter Carter, RCN chief executive and general secretary, said: "These responses illustrate that despite the recent attention which has been drawn to the importance of whistleblowing, many nurses are still experiencing a culture of fear and intimidation if they try to speak out. This is putting patient safety at risk.
"One of the key lessons from the Francis report was that frontline staff must feel confident they can raise concerns about patient safety without fear of reprisals."
Just under half (45%) of those respondents who had raised concerns said their employer took no action, while about a third (32%) said they didn't know whether their organisation had a whistleblowing policy.
Of those respondents whose organisation did have a whistleblowing policy, 37% were not aware that there is legal protection for all employees who raise concerns.
Poulter said: "We want all staff working within the NHS to feel able to speak up and raise concerns, and every NHS organisation to take concerns seriously and act on them.
"That is why we have funded a national helpline for whistleblowers, strengthened the NHS constitution and provided stronger protections for whistleblowers in NHS staff contracts."
Poulter added: "We are also giving NHS organisations a new duty to be open if things go wrong, to help build a far more open NHS culture."
Carter said: "Nursing staff want to provide excellent care, but sometimes the systems they work in do not allow this. Staff know what is safe for their patients and what is not.
"However, they cannot raise concerns if they feel unsure about what their employer's policy is or what the repercussions will be."
Carter added: "In particular, nurses have told us about occasions when they have been bullied, ostracised or belittled when they have tried to raise concerns on behalf of their patients.
"The stakes are simply too high for this to be allowed to continue. Trusts which don't encourage an open culture from the very top will only continue to make mistakes, sometimes with devastating consequences."