The officer, who was in Canada on a temporary posting, has been bailed to appear in court on 15 September.
An army spokesman said it was aware of an investigation involving a serving British army officer.
The alleged assault occurred at Fort Frontenac, in Kingston, following commemorations for the World War One Battle of Vimy Ridge, on 9 April, police said.
The alleged victim – a 52-year-old female officer – had attended a military function at the fort.
She then allegedly went to a bar with other guests, including Lt-Col Davies. Police say she reported having being sexually assaulted in her hotel room in the early hours of the following day.
Lt-Col Davies was arrested and charged earlier this week.
He has since been released but was ordered to surrender his passport and has been barred from leaving Ontario ahead of a court appearance.
“We are aware of an investigation being conducted by Kingston Police into an alleged incident that took place in April this year involving a serving British army officer,” a British army spokesman said.
“As the case is sub judice it would be inappropriate to make any comment.”