The Police Investigations and Review Commissioner (Pirc) is assessing the complaint against Chief Constable Phil Gormley which is understood to have come from Martin Leven, Police Scotland’s head of IT.
Mr Leven was signed off sick after making a complaint about David Page, the force’s most senior civilian last year.
It is thought the allegation about the chief constable’s behaviour is part of the separate complaint made against Mr Page.
A spokesman for Burness Paull, which is representing Mr Gormley, said: “We are aware that a single allegation of misconduct dating back almost one year has been referred by the SPA’s complaints and conduct committee to the Pirc for assessment.
“Chief Constable Gormley entirely denies the allegation as spurious and contrived. The chief constable is disturbed by the timing of this allegation arising and it gives rise to serious questions in light of recent political debate about his employment status.”
It emerged last month that the SPA board approved Mr Gormley’s return to work before an “intervention” by justice secretary Michael Matheson. The SPA made its decision without consulting with the Pirc or Police Scotland about Mr Gormley resuming his duties.
Former SPA chairman Andrew Flanagan is expected to be questioned by MSPs on Holyrood’s audit committee next week, the same day the current board is due to decide on whether Mr Gormley’s period of leave should be extended.
Mr Gormley has been on leave since September while the Pirc carries out three separate investigations into alleged bullying. He continues to receive his £214,000-a-year salary.
The latest complaint, which is understood to be the sixth made against the chief, would take the number of investigations to four, if a formal inquiry is deemed necessary.
Mr Gormley faces dismissal if allegations of gross misconduct are proven.