Assistant Chief Constable Bernard Higgins is now being investigated over misconduct allegations, it has emerged.
The Police Investigations and Review Commissioner (Pirc) received anonymous claims about Mr Higgins in October.
An investigation into criminal allegations was launched in November, and a second investigation is now under way into the misconduct claims.
Mr Higgins, who was suspended in November along with three other officers, has denied any wrongdoing.
The Pirc said that if proven, some of the accusations would amount to misconduct and others would amount to gross misconduct.
A statement issued by lawyers acting on behalf of Mr Higgins said the notice of investigation served by Pirc “contains no new allegations”.
It added: “ACC Higgins will provide a full response to the allegations at the earliest opportunity. He strenuously denies any misconduct and is keen to resume his duties as soon as possible.”
His lawyers also said that one investigation was taking place, which was reporting to two different masters.
The police watchdog is currently carrying out an investigation into criminal allegations facing Mr Higgins and three other officers – Supt Kirk Kinnell, Ch Insp Bob Glass and Sgt Cat Gibbons.
The probe was launched on 24 November after the Crown Office and Procurator Fiscal Service (COPFS) sanctioned the move. All four officers have been suspended.
One of the allegations being examined by the criminal investigation is that.
The precise nature of the misconduct and gross misconduct allegations against Mr Higgins are not known.
Until now the claims were simply being considered, but Pirc has now decided that they merit a separate misconduct investigation.
The Pirc confirmed the allegations of misconduct against Mr Higgins were initially referred by Commissioner Kate Frame to the Scottish Police Authority (SPA) on 18 October.
In November, the SPA referred the allegations of misconduct back to the Pirc.
Notice of investigation
A Pirc statement said: “Following its initial assessment the SPA indicated that, if proved, these allegations would amount to gross misconduct and took the decision to suspend the officer.
“The commissioner assessed the various allegations and considers that some, if proved, would amount to gross misconduct and others, if proved, would amount to misconduct.”
Mr Higgins was served with a notice of investigation on Thursday and informed that he is the subject of a misconduct inquiry.
When the Pirc has concluded its investigation the commissioner will submit a report about the criminal allegations to the Crown Office.
A separate report in relation to the misconduct claims will be submitted to the SPA.
It will include a summary of evidence and an opinion on whether the allegations against Mr Higgins should be referred to an internal misconduct hearing.