Union leaders also claimed that senior Scottish Government figures would have been aware of previous concerns raised among staff over dealings with ministers.
The claims emerged as a specially convened committee of MSPs, looking into the Scottish Government’s handling of complaints against former First Minister Alex Salmond, took evidence from civil service union representatives.
Dave Penman of the FDA union warned that there were "significantly more complaints" about ministerial behaviour in Scotland.
He told MSPs that about 30 cases were raised over the past decade concerning Scottish ministers, across "multiple" administrations, even predating the current SNP regime.
"That is an issue about culture, about the approach from those who have responsibilities for the process and essentially how that process is applied," he said.
"We would indicate that the issues that we talk about are not historical - they're current," he said.
"From our issues and our evidence, the issues we're talking about are extant in relation to the conduct of ministers around civil servants."
Mr Penman said the level of complaints which the union had received from civil servants Scotland was "extraordinary and remarkable" and higher than other civil service departments around the UK.
And he acknowledged the level of concern may stretch beyond those individuals who have come forward.
The Scottish Government's top civil, Permanent Secretary Leslie Evans, said she did not recognise the union's claims of a "climate of fear" among staff during a recent appearance before MSPs. But Mr Penman today insisted the senior Scottish Government figures will have been aware of the issue.
"If you look at the numbers we're talking about, I think, over a decade, it seems to me that people inn the Scottish Government were probably aware there were issues.
"You can't look at that number of concerns and say that everyone thought everything was fine.
"Whether that's something that perhaps should have been addressed earlier either by ministers or those within positions of authority within the civil service is an interesting point.
"But I wouldn't think this should come as much of a surprise to people working in the Scottish Government."
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