A TRADE union boss who said there was a "culture of fear" in Alex Salmond's government has defended his description and insisted there are ongoing issues relating to bullying and staff confidence in the complaints process in the current administration.

FDA general secretary Dave Penman said he had "thought very carefully" in his written submission to the committee, published last month, when he gave evidence to MSPs today.

During her appearance at the inquiry two weeks ago Scotland's top civil servant Leslie Evans said she did not recognise the way Penman had described the Scottish Government's working environment.

Penman was asked about Evans's remarks and whether he was surprised about her rejection of his description.

READ MORE: Leslie Evans 'very willing' to discuss Alex Salmond allegations

"Quite often the information and the context we get as trade unions is different from the context and information management get in an organisation," he replied.

"People will talk to a trade union in a way they may not with their manager or senior manager, so it doesn't surprise me at times that there can be a different perception of what is going on among the most senior people in an organisation and those who are … working in it on a day to day basis."

He added: "We thought very carefully about the language we used in our evidence. We sought to summarise a long period of time within Scottish Government and tried to talk about the culture of the organisation over a decade."

Earlier as he gave evidence Penman said that the FDA’s concerns over the Scottish Government working culture were still relevant today.

"It doesn't seem to be changing behaviour which is part of the point of these processes about stopping people being bullied in the first place…that is an issue about culture," he said.

"We would not say that people still have confidence in the process for dealing with complaints, we would indicate that the issues that we talk about are not historical...and therefore that can only be a failure of how that policy has been applied," he said. "It's quite clear from us…that the issues we are talking about here are extant."

Today's hearing is the third oral evidence session being heard by the Committee on the Scottish Government Handling of Harassment Complaints.

In written evidence ahead of their appearance before MSPs, Penman said the FDA had raised numerous concerns a decade ago about the culture and "bullying behaviour" in the First Minister's office and other ministerial departments.

Penman wrote: "The culture within the former First Minister's Office and other ministerial offices in relation to bullying behaviour became a concern for us and was raised with successive permanent secretaries.

"Although action was taken and short-term improvements or apologies were made, this did not bring about an overall change in culture.

"Some civil servants expressed to us that they were operating in a culture of fear and were unable to speak truth unto power and discharge their duties effectively."

The written submission revealed that approximately 30 union members have made complaints about five ministerial offices in the past 10 years.

Penman added that union members "did not trust (the Scottish Government) to handle complaints effectively" or to ensure confidentiality of the complainants, fearing that raising formal complaints would be "detrimental" to their careers.

The Holyrood investigation into the handling of harassment claims was launched following the unlawful attempt to investigate claims made against Salmond.

A legal challenge by the former first minister - who was also cleared in court of 13 charges of sexual assault - led to a judicial review at the Court of Session that found the process had been "tainted by apparent bias" because of contact between the lead investigator and some of the accusers.

As a result, the Scottish Government had to pay more than £500,000 for his legal costs.

The inquiry has so far heard from Evans, as well as James Hynd, the head of the Cabinet, Parliament and Governance Division within the Scottish Government, and Nicola Richards, the Scottish Government's director of people.