A malfunction of the boat's global positioning system (GPS) is likely to have been responsible for the vessel straying off course, the spokesman added.
The incident comes at a time of rising tension between the two Koreas, following Pyongyang conducting a nuclear test as well as test-firing ballistic missiles earlier this year.
A South Korean worker employed at a jointly operated industrial complex in North Korea has been detained for more than 120 days for allegedly speaking ill of the Pyongyang regime.
The North is also holding two American journalists who were detained at its border with China in March and later found guilty of hostile acts against North Korea.