The officer, understood to be Temporary Assistant Chief Constable Pat Campbell, was suspended from Wednesday, force oversight body the Scottish Police Authority (SPA) said.
He was previously a public protection officer in the Edinburgh division.
Prosecution service the Crown Office has instructed police watchdog the Police Investigations and Review Commissioner (Pirc) to investigate the allegation.
A senior officer can be suspended if an allegation, if proven, would be sufficiently serious to amount to misconduct or if the nature of the allegation means suspension is in the public interest.
The SPA said in a statement: "The Scottish Police Authority has suspended a senior officer from Police Scotland duties.
"The decision was taken after a criminal allegation was brought to the authority's attention.
"The Police Investigations and Review Commissioner is investigating this allegation under direction from the Crown Office and Procurator Fiscal Service.
"The suspension is effective from Wednesday 1 December and will be reviewed regularly, or if there is a change in circumstances relevant to the suspension."
Mr Campbell's role, which he took up a year ago, is executive lead for organised crime, counter-terrorism and intelligence, which also covers border policing, cyber crime and digital forensics.
He is senior responsible officer for cyber capabilities, cyber strategy and technical surveillance.
He joined Strathclyde Police in 1995, ahead of the merger of Scotland's eight forces in 2013 to form Police Scotland.
When the forces merged, he was a detective superintendent working in public protection and divisional crime in Edinburgh.
In August 2018 he was promoted to detective chief superintendent and appointed strategic lead for specialist crime support.