An official with the Seoul Central District Court said that it had issued the warrant to arrest the executive -- identified only by his surname Yoon.
Charges include manipulating documents on emissions tests to get approval for selling Volkswagen vehicles in the country.
Prosecutors plan to question Yoon on whether he was acting under orders from Volkswagen's German headquarters, Yonhap news agency said.
The world's second-largest automaker faces legal action in several countries, after it admitted in September to faking US emissions tests on some of its diesel-engined vehicles.
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Foreign carmakers, especially German brands like Volkswagen, have steadily expanded their presence in the South's auto market long dominated by the local giant Hyundai and its affiliate Kia.
Sales of foreign cars account for about 15 percent of total auto sales, compared to 10 percent in 2012.
Around 70 per cent of foreign auto sales in South Korea are diesel-engined vehicles.