The June preliminary data released by the Ministry of Trade, Industry and Energy compared with a 3.2 percent increase in exports in May year-on-year.
The ministry said the June decline was attributable to fewer working days compared to the same month of last year, Yonhap News Agency reported.
South Korea, Asia's fourth-largest economy after China, Japan and India, is heavily dependent on exports.
The government also remains concerned about the declining yen which makes Japanese goods cheaper in markets where South Korean products compete.
Despite lower exports in June, the country earned a trade surplus of $5.52 billion as imports for the month also were down 1.8 percent to $41.21 billion, Yonhap News Agency reported. June represented the 17th straight month of trade surplus.
In the first six months of this year, South Korea has earned a trade surplus of $19.6 billion.