The government plans to set up the unification account in an inter-Korean cooperation fund that is currently worth about 1 trillion won (US$869 million).
The fund already has a separate account earmarked for inter-Korean projects, according to the Unification Ministry in Seoul, which handles North Korean affairs.
Unification Minister Yu Woo-ik made the announcement during a meeting with South Korean reporters on the last day of his three-day trip to Beijing.
The development underscored Seoul's longstanding commitment to unifying with North Korea. The envisioned account, which needs parliamentary endorsement, is part of South Korea's efforts to help cushion the cost of re-unification with one of the poorest countries in the world.
A state-run think tank has estimated that the initial costs for the integration of the two Koreas could range from 55 trillion won (US$47 billion) to 249 trillion won ($216 billion).
The estimate, which is projected to cover the first year of integration, was based on the assumption that the two neighbors could be unified two decades from now, according to the Korea Institute for National Unification.
Yu said the government does not have an immediate plan to levy a tax on citizens to help finance the potential unification, though he left open the possibility of collecting a tax.
South Korea has been working on details of a so-called unification tax since last year when President Lee Myung-bak floated the idea of using taxpayer money to help finance unification.
Seven out of 10 South Koreans believed that the costs of unification would outweigh its benefits, according to a recent telephone survey, in the latest sign of public concern over re-unification's economic burden.
The National Unification Advisory Council, a presidential advisory body on unification, released the results of last week's poll of about 1,000 people.
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Yu was to return home later Wednesday after a three-day trip to Beijing aimed at enhancing Chinese understanding of the situation on the Korean Peninsula and bolstering ties with the North's key ally and the world's No. 2 economy.
Yu sought Chinese cooperation in handling North Korean defectors during his meeting with former state councilor Tang Jiaxuan on Wednesday, a day after he made a similar appeal to Foreign Minister Yang Jiechi.
Tens of thousands of North Korean defectors are believed to be hiding in China, hoping to travel to Thailand or other Southeast Asian countries before resettling in South Korea.
China does not recognize North Korean refugees and repatriates them back to their homeland, where they could face harsh punishment and even execution, according to defectors and activists.
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