Seoul military officials initially suggested the item was a drone from North following the incident on Tuesday, before saying Wednesday that balloons carrying propaganda leaflets had blown in across the frontier, one of the most fortified locations in the world.
North Korea said on Monday it had successfully tested an intermediate-range ballistic missile to confirm the reliability of the late-stage guidance of the warhead, indicating further advances in the ability to hit United States of America targets.
Seoul said its military fired an unspecified number of warning shots on Tuesday after detecting an object flying across the border.
The identity of the object remained unclear, the military said, but Yonhap news agency said it was possibly a drone, more than 90 shots were fired in return and it disappeared from radar screens.
The suspected North Korean balloons were spotted two days after Pyongyang test-fired a ballistic missile - its second missile test in seven days.
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The test was led by the Missile Defense Agency , and it also included the Air Force's 30th Space Wing at Vandenberg and U.S. Northern Command, which oversees the defense of the United States at home.
The administration of US President Donald Trump has said military action was an option under consideration, sending fears of conflict spiralling. The ground-to-ground missile reportedly flew some 500 kilometers (310 miles) before falling into the Sea of Japan short of reaching Japan's exclusive economic zone. A day later, it said that it was probably a balloon.
South Korea, in turn, is anxious about Pyongyang's continuing nuclear and missile tests.
Since taking office this month, President Moon Jae-in, of the Democratic Party of Korea, is taking a more moderate approach to the North compared with those of two previous presidents, expressing his willingness to meet with North Korean leader Kim Jong Un under the right conditions and making conciliatory gestures.
The North's official KCNA news agency, citing the spokesman for the foreign ministry, said the country had "substantially displayed" the capabilities for mounting a nuclear attack on Hawaii and Alaska and had built full capabilities for attacking the United States mainland. The reclusive country warned the USA about its recent military drills with South Korea as well as its missile defense system, THAAD, installed in South Korea in April.
North Korea a week earlier successfully tested a new midrange missile - the Hwasong 12 - that it said could carry a heavy nuclear warhead.