Seoul sent three North Koreans who crossed the maritime border in a fishing boat back home on Monday after they said they wanted to return, the Unification ministry said.
"All of the three crew members, as well as the wooden vessel, will be returned to the North," the ministry told reporters in Seoul.
The boat and three crew had set off, a ministry official told AFP.
The vessel had a white towel tied to its mast when it crossed the Northern Limit Line in the East Sea, also known as the Sea of Japan, into South Korean waters late Saturday.
Thinking the towel might be a sign the crew wanted to defect, South Korean authorities took the boat to a military port for investigation.
But when questioned the crew said they had crossed the border by mistake and wanted to go home, the ministry said.
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The incident comes after a North Korean fishing boat crossed the intensely monitored border undetected in June and sailed into a South Korean port before it was identified.
Two of the four crew members said they wanted to defect and the other two were sent back to the North. A South Korean general was sacked over the lapse in border security.