North Korean refugees now living in the South have won the right to avoid identification as such in their official papers. It had previously been possible to infer someone's origin from the number.
The Unification Ministry in Seoul, which handles inter-Korean affairs, said they would now be allowed to change their social security numbers.
In a survey carried out three years ago, two thirds of North Korean defectors said they had faced workplace discrimination over their background.
South Korean-born citizens are given numbers associated with their birthplace. But North Korean refugees have until now been allocated numbers based on the area code of the heavily-guarded Hanawon resettlement centre near Seoul. The centre is used to educate North Koreans about life in the South and help them to integrate into South Korean society.
South Korea's Yonhap news agency reported that the change in law also made settlement grants available to defectors who have stayed abroad for more than 10 years after leaving North Korea.
More than 15,000 defectors have arrived in South Korea since the Korean war of 1950-53, said Yonhap.