The inspector, who has not been publicly named, is also accused of stalking involving serious harm and distress.
He was arrested on 22 August by Sussex Police, who are leading the investigation.
“The allegations do not relate to the officer’s role as a royalty and specialist protection command officer,” a spokesperson for the Metropolitan Police said.
“The officer has been placed on restricted duties.”
Scotland Yard said it made a mandatory referral to the Independent Office for Police Conduct, but the watchdog referred the case back to its internal professional standards department.
The royalty and specialist protection command is charged with guarding the royal family, prime minister, government ministers, ambassadors and visiting heads of state.
It also provides armed officers at royal palaces in London, Windsor and Scotland.
No details of the arrested man’s role within the branch have been given.
A spokesperson for Sussex Police said its officers arrested the man at a residential property in mid-Sussex.
“The 47-year-old man was released on police bail until 19 September while enquiries are ongoing,” a statement added. “The two people are known to each other.”