The report comes amid heightened fears of conflict on the Korean peninsula, fuelled by US President Donald Trump's continued threats of military action against Pyongyang to tame its weapons ambitions.
The bombers took off from the US Pacific territory of Guam on Tuesday night, before entering South Korean airspace and conducting firing exercises over the East Sea and Yellow Sea, South Korea's military said.
Tuesday's decision adds that all North Korean citizens "are suspected of generating revenue which is used to support the country's illegal nuclear and ballistic missile programmes".
The ministry said that there are no specific signs that confirm North Korea's reopening of the factory zone, though some bus movements and illuminated street lamps have been spotted.
The constant threat of war against North Korea's adversaries is so integral to Kim Jong Un's regime that state media are dominated by it and national events are marked with military parades and missile tests.
But neither side is budging in the standoff.
The North has test-fired dozens of missiles, including two ICBMs in July.
North Korean hackers stole a large amount of classified military documents, including South Korea-U.S. wartime operational plans to wipe out the North Korean leadership, a South Korean ruling party lawmaker said yesterday. Last month he got China to agree to new U.N. Security Council sanctions on North Korea.
The South Korean companies that operated in Kaesong also benefited by employing low wage North Korean workers to produce labor-intensive goods, such as clothes and utensils. But Kim, the third generation of his family to rule, is officially revered in the North, and any suggestion of removing him from power is taken extremely seriously in Pyongyang.
Tensions have soared between the United States and North Korea following a series of weapons tests by Pyongyang and a string of increasingly bellicose exchanges between Trump and North Korean leader Kim Jong Un.
Last week Trump stepped up his attacks on the North saying that talking with it does not work and "only one thing will work".
"The Korean-American relationship is very important and our visit to Chinhae gives us the opportunity to strengthen the outstanding relationship that exists between the U.S. and [South Korea]", said Cmdr.
"I think I have a little bit different attitude on North Korea than other people might have", he told reporters at the start of talks with Canadian Prime Minister Justin Trudeau at the White House. And the count will continue to rise.
A South Korean presidential official said Tuesday's operation was part of a recently agreed upon rotational deployment of U.S. military assets to the peninsula, according to the Yonhap News Agency.
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