Fergus Ewing, the Rural Economy Secretary, confirmed today that a "process" is now underway after the claims brought by staff, believed to be with Marine Scotland.
Complaints of bullying behaviour by the minister late last year, Sky News has reported.
Mr Ewing said today: "I completely reject all claims against a me.
"A process is underway and that is entirely right and proper when such allegations are made.
"That process is at an early stage. I will make no further comment while that process is ongoing."
The Scottish Government's ministerial code, which asserts that "bullying... will not be tolerated", states that "The First Minister is... the ultimate judge of the standards of behaviour expected of a Minister and of the appropriate consequences of a breach of those standards."
It's understood that senior managers in the Scottish Government have been attempting to resolve the issue informally.
The complaints procedure allows for an escalation of the process, which would involve a formal complaint as a next step.