The three men, three women and three children were picked up by Japan's coastguard on September 13. They said they had spent five days at sea after leaving the North's east coast in a rare seaborne defection.
The nine will undergo the normal interrogation by intelligence authorities before being sent to a resettlement centre, a foreign ministry spokeswoman in Seoul told AFP.
The group, which was travelling in an eight-metre (26-foot) wooden boat off Japan's west coast, was led by a man who said he was a member of the North's People's Army.
South Korea has said it will handle the issue in a humanitarian way in accordance with the nine North Koreans' own wishes.
Hundreds of North Koreans each year flee hunger or repression in the isolated communist state, but the vast majority cross the border on foot to China before travelling to the South via a third country.
More than 21,700 have arrived in the South since the 1950-1953 war, the vast majority in recent years.
They have automatic citizenship in the South but must spend three months in a resettlement and education centre when they arrive.