The director of the country's legal investigation bureau, OJI, Walter Espinoza gave a press conference to explain the deaths had occurred in the areas of Bagaces and Upala, the most affected by the strong rains and winds, Xinhua news agency reported.
"The official number of deaths...is nine. Five of these deaths happened in the canton of Upala, and four in the zone of Bagaces," he explained.
Costa Rica's President Luis Guillermo Solis attended the same press conference and said his government had decreed three days of national mourning, starting November 28, to allow time for search and rescue efforts.
According to Solis, the north of Costa Rica saw a monthly amount of rain fall in just six hours.
Neighbouring Nicaragua, which was also hit by Otto, reported no casualties although a number of buildings were destroyed or damaged.
On Friday, Otto moved out into the Pacific Ocean, where it was downgraded to a tropical storm.