Around 20% of people who have reported wrongdoing in the workplace have suffered a reprisal.
However, a larger proportion of whistleblowers say they have seen the benefit of raising their concerns.
The data is contained in a new report from Transparency International Ireland which looks at the experiences of 600 people who had contacted them about exposing activities in their industry.
When looking at retaliation against whistleblowers, the health sector accounted for the largest number of calls from people who suffered from reporting wrongdoing.
This was followed by An Garda Síochána and then those working in banking and finance.
John Devitt, Chief Executive of Transparency International Ireland, said a "significant" but minority of whistleblowers report suffering retaliation in the workplace.
He told the Moncrieff programme: "Employers on a whole will act on the concern raised by their employees but in a significant amount of cases, albeit a minority of them, people do suffer some sort of a reprisal from blowing the whistle.
"This will largely be down to the culture of the organisation, the type of concern they are raising and the person they are blowing the whistle on, because if the stakes are high, there is much more reason for people to make life difficult for someone who speaks up."
Mr Devitt said the two biggest reasons why people don't speak up is fear of retaliation and fear of futility, that they will have wasted their time in raising a concern.
Such reprisals can include formal sanctions such as disciplinary actions, as well as informal ones which are more difficult to identify such as not being invited to social functions or being isolated from colleagues.
He added that new rules are due to come into effect following a European Directive which will require employers to respond to employees who have raised a concern within a set period of time and also report how they responded to the reported wrongdoing.
This will apply to both the private and public sector and Mr Devitt is hopeful that it will result in some cultural change in Ireland with relation to whistleblowers.