The man was apprehended Tuesday night while lying on a bank of the Han River, which is in a restricted military area near the border, said the official, speaking on condition of anonymity due to office policy.
The man was in his late 20s or early 30s, Yonhap news agency said, and had told investigators that he tried to go to North Korea to meet leader Kim Jong Un.
Americans are occasionally arrested after entering North Korea illegally from China but a U.S. Citizen trying to get in from South Korea is unusual.
In 1996, American Evan C. Hunziker entered the North by swimming across the Yalu River that marks the Chinese border.
Hunziker, who apparently made the swim on a drunken dare, was accused of spying and detained for three months. Hunziker, 26 at the time, was eventually freed after negotiations involving a special U.S. Envoy.
The North Koreans wanted to slap Hunziker with a USD 100,000 criminal fine but eventually agreed on a USD 5,000 payment to settle a bill for a hotel where he was detained. He killed himself about one month after his release.
Last year, South Korean soldiers shot and killed a man with a South Korean passport who officials said ignored warnings while swimming across the Imjin River toward North Korea.
Some recent U.S. Detainees include missionaries aiming to spread the gospel in North Korea or draw attention to the country's alleged human rights abuses.
On Christmas Day in 2009, Korean-American missionary Robert Park defiantly walked into the North from China calling for dismantling of the North's prison camps. Park, who was deported from the country in February 2010, has said he was tortured by interrogators.
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