Senior Sergeant Brian Benn said no-one else was being sought.
The incident allegedly occurred in a room at the hotel, in Queens Gardens.
Police said the woman was taken to Dunedin Hospital for a medical check.
The man (50) was believed to have been found near the hotel.
About six marked police cars, at least two unmarked vehicles and a police dog van swooped on the hotel after the alarm was raised at 8.35pm.
Police officers, including a dog handler with police dog, entered an accommodation wing about 8.50pm.
A distressed woman was escorted from the hotel by police soon afterwards and driven away in a police car.
The hotel was cordoned off while police spoke to the occupants.
Police said there was nothing to suggest the incident was linked to two sexual assaults in Dunedin last weekend.
