The storm, which began on Tuesday, flooded many parts of the country, prompting 60 patients to be evacuated from two hospitals by government helicopters.
"Nine died in the storm and about 200 were injured. In some parts of the country, the water level was six feet (about 1.80 metres) high," a rescue services spokesman said.
The two hospitals had to be closed.
"My estimate is that it will cost no less than 20 million rials ($50 million) to put them right," a doctor said.
Witnesses said cars were swept away as rainwater flooded major motorways. Some drivers scrambled to the rooftops of their cars to escape the rising water.
The meteorological office said the storm would continue until Saturday.
Oman was hit by cyclone Phet last year, which killed about 50 people in different parts of the sultanate.