The typhoon was the worst in the country for 40 years, and property damage is estimated at more than $1bn.
A government official told Reuters news agency that the clean-up will require twice as much money as remains for disaster relief in the state coffers.
RUSA's WRATH:
Typhoon Rusa has also affected North Korea, leaving thousands homeless and destroying more than 80,000 tonnes of crops, according to official figures.
But the figures - from the North Korean Red Cross - made no mention of "scores" of deaths reported by the official KCNA agency.
Rusa, the Malaysian word for deer, destroyed bridges, railway lines, roads and homes as it swept through the country at the weekend.
President Kim Dae-jung has declared four areas disaster zones and has pledged 150bn won ($125m) in emergency funding.
The National Disaster Prevention Headquarters estimates 2.13 trillion won of damage has been done.
The country's upcoming Asian Games, due to begin at the end of September, could also be affected.
Several sports facilities, including part of a field hockey stadium, were severely damaged at the games' site in Busan, south of the country.
Eye disease
Conjunctivitis, a highly contagious eye disease, has swept through South Korea accelerated by the breakdown in sanitation and spread to the games' training camp.
Twenty-one athletes have been sent home so far and the chief team doctor urged the organising committee to send a health alert to all 42 countries due to participate in the competition.
About 170,000 children have also been affected by the disease, forcing the closure of 70 schools nationwide.
Asia braces for more
Red Cross talks due to take place between North and South Korea this week on family reunions have been delayed as a result.
Rusa is the most powerful storm to hit the Korean peninsula since Typhoon Sarah in 1959, which left more than 840 dead or missing.
Meanwhile, another typhoon is heading for north-east Asia.
Typhoon Sinlaku, with surface winds of 144 kilometres an hour (89 mph) is due to hit Taiwan and the Japanese islands of Okinawa late on Wednesday or early Thursday.