The North's official Korean Central News Agency (KCNA) said US citizen Pae Jun-Ho had admitted to the charges and would soon face "judgment".
Pae was arrested in November as he entered the northeastern port city of Rason, which lies inside a special economic zone near North Korea's border with Russia and China.
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The announcement follows a months-long standoff on the Korean peninsula stoked by the North's nuclear test in February, which prompted the UN Security Council to impose fresh sanctions on the isolated nation.
KCNA said a "preliminary inquiry" had been completed for Pae.
"He admitted that he committed crimes aimed to topple the DPRK (Democratic People's Republic of Korea) with hostility toward it. His crimes were proved by evidence.
"He will soon be taken to the Supreme Court of the DPRK to face judgment," according to the report, which did not say what the charges were based on.
South Korean media in December identified the detainee as a 44-year-old Korean-American tour operator.
He was travelling with five other tourists and was detained when a computer hard disk was found among the group's belongings, according to the South Korean newspaper Kookmin Ilbo.
Several Americans have been held in North Korea in recent years.
In 2011, a US delegation led by Robert King, the US special envoy for human rights and humanitarian issues, secured the release of Eddie Jun Yong-Su, a California-based businessman, who had been detained for apparent missionary activities.
In 2010, former US president Jimmy Carter won plaudits when he negotiated the release of American national Aijalon Mahli Gomes, sentenced to eight years of hard labour for illegally crossing into the North from China.
On another mercy mission a year earlier in 2009, former president Bill Clinton won the release of US television journalists Laura Ling and Euna Lee, jailed after wandering across the North Korean border with China.
Relations between the two Koreas have worsened markedly in recent months, with Seoul announcing on Friday a complete withdrawal from a jointly run industrial park in the North.
The move plunged into doubt the future of the Kaesong complex -- once a rare symbol of cooperation across the world's most heavily militarised border, and a crucial source of hard currency for Kim Jong-Un's isolated regime.
South Korea said Friday that it had decided to pull its remaining 175 workers from the site after Pyongyang rejected its ultimatum to join formal negotiations on restarting the stalled operations.
A spokeswoman for the Unification Ministry said 127 workers were expected to cross back over the border in two convoys of vehicles on Saturday afternoon.
The remaining 48 people -- mostly government employees who manage the complex as well as telecom and electrical engineers -- would be pulled out on Monday, she said.
But a businessman with interests in Kaesong said many of the 123 South Korean companies who usually operate there were resisting the move.
"Some say we should comply with the government request to pull out but many others do not want to leave for fear of losing their investment," he told AFP, asking not to be named.
Established in 2004, the complex lies 10 kilometres (six miles) inside the North, which remains technically at war with the South after the 1950-53 Korean War was concluded with a ceasefire rather than a peace treaty.
