Scottish Rural Economy Secretary Fergus Ewing has "completely rejected" claims of bullying made against him by staff.
Sky News had reported that complaints were made by civil servants based in Edinburgh late in 2019.
Mr Ewing - whose ministerial role was expanded by Nicola Sturgeon in a recent reshuffle - confirmed that a formal investigation process is under way.
But he told reporters at Holyrood that he rejected "all claims against me" and said he would make no further comment.
The Scottish government's code of conduct for ministers states that bullying "will not be tolerated", and there is a specific "fairness at work" policy process for handling complaints made by employees.
This could ultimately see Deputy First Minister John Swinney and Permanent Secretary Lesley Evans consider the case.
Asked about the reports at Holyrood on Thursday, Mr Ewing said: "I completely reject all claims against me.
"A process is under way, 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 whilst that process is ongoing."
Mr Ewing's rural economy portfolio was expanded to include tourism on Monday, as the Scottish cabinet was reorganised following the resignation of Derek Mackay.
Ms Sturgeon's spokesman said the first minister was aware of the investigation during the reshuffle, but said she would not have given Mr Ewing the extra brief if she did not think such a move was appropriate.