Paul Gray, director general for health and social care in Scotland, said he did not object to people like Professor June Andrews, a renowned dementia expert, raising concerns.
However, he added: "I am not sure I fully recognise the suggestion that there is somehow a culture of trying to suppress information."
Ms Andrews, director of the Dementia Services Development Centre at Stirling University, spoke out in The Herald last month over her concerns that people were being given a false picture of hospital care.
She said: "Managers and politicians are in a painful situation where they have to collude in an attempt to present to the public a picture of hospitals that is completely unrealistic.
"The Scottish Government already knows that there are some problems in hospitals but it is not generally known what the scale of the problem is. We need a more open discussion about the fact that a hospital is not a safe place."
Discussing the need for candour about issues in the health service, Mr Gray, who is also chief executive of NHS Scotland, highlighted ways in which he believed the service had become more transparent and open to criticism.
These included health boards working with the feedback website Patient Opinion Scotland, the National Confidential Alert Line which has been set up for Scottish NHS staff to report concerns and the action taken by Alex Neil, health secretary, to stop health boards asking employees to sign gagging clauses when they leave their posts.
He said: "Genuinely if there is more that we can do to enable patients, carers and staff to feel confident about speaking out I would want to do that."
He later added: "I have said if we do something wrong we should apologise. We should not put at the front of our minds 'will this lead to legal action or a complaint?' We should put in the front of our minds, 'how did this affect the individual?' and if it affected them badly I would want to apologise."
A patient safety programme has been rolled out across Scotland which includes hospital mortality rates being monitored and published regularly. This sparked a review of care in NHS Lanarkshire last year.
Mr Gray concluded: "There is considerable evidence of excellent services provided day in day out across Scotland. We should therefore feel confident in recognising the small number of cases where things do not go as well as they should and we should be confident in explaining what has happened with a view to ensuring we continue to improve."
Explaining her comments, Professor Andrews said she believed that there were "political repercussions from speaking about certain things that we do well to avoid, and not always out of self-interest, but because the torrent of sometimes ill-informed, and sometimes malevolent, exchanges that are likely to flood into the public space doesn't always help those we care about - patients, families and staff working in the system."
Describing the way some hold back from speaking out, she said: "A relative or patient sometimes worries whether they'll be victimised. They just want to get away.
"A whistleblower really has to consider whether they have the time, and resilience to undertake that act. They need to consider whether their own delay in blowing the whistle means that they are personally compromised and to blame. Who is going to through the first stone?
"A responsible commentator has to consider whether bringing down a minister or a government through critical comment of the health system guarantees that the next minister or government will do it better."