Kim Yeon-chul, South Korea's point man for relations with the North, resigned over heightened tensions on the peninsula days after Pyongyang blew up its liaison office with the South.
South Korean President Moon Jae-in on Friday accepted the resignation of the minister responsible for relations with North Korea, as tensions with Pyongyang rise over the activities of defectors in the South and stalled diplomacy.
South Korean Unification Minister Kim Yeon-chul, who oversees engagement with North Korea, offered on Wednesday to step down, making himself accountable for the worsening ties.
After seeing a boost in favourability over his government's handling of the coronavirus outbreak, Moon's approval rating fell to 55 percent, the lowest level in about three months, driven by worries over North Korea, according to a Gallup Korea poll released on Friday.
North Korea has snubbed Seoul's calls for engagement as efforts to restart inter-Korean economic projects stalled due to international sanctions designed to rein in the North's nuclear and missile programmes.
Pyongyang has also taken issue over defectors in the South sending propaganda leaflets into North Korea.
Citing South Korea's failure to stop the defectors, North Korea this week blew up the joint liaison office on its side of the border, declared an end to dialogue with South Korea and threatened military action.
Unification Ministry spokeswoman Cho Hye-sil told a briefing on Friday that an emigre planning to send hundreds of bottles stuffed with rice, medicine and medical face masks to North Korea by throwing them into the sea near the border on Sunday, had been asked to abandon its plan.
She warned that authorities would stop the group, and others like it, from carrying out such plans, and would seek to impose penalties for violations of a law governing inter-Korean exchanges and cooperation.
After a flurry of barbed statements earlier this week, North Korean officials did not issue direct criticism of South Korea for a second day in a row on Friday.
But state media kept up steady stream of reports on North Koreans "exploding with anger" at the South.
Analysts say the North may be seeking to manufacture a crisis to increase pressure on the South to extract concessions.
Inter-Korean relations have been in deep freeze for months, following the collapse of a summit in Hanoi between North Korean leader Kim Jong-un and US President Donald Trump.
That meeting foundered on what the nuclear-armed North would be willing to give up in exchange for a loosening of sanctions.
A pro-engagement academic and a longtime confidant of Moon, Kim was appointed to the post in March last year, days after the Hanoi meeting.
Reports say John Bolton, the former US national security adviser, criticised Moon in his new memoir for encouraging both Kim and Trump to have unrealistic expectations of the other.
Moon, who has also long backed engagement with the North, has been called unrealistic by his critics for his dovish approach.
On Monday the left-leaning president gave a speech calling for inter-Korean dialogue and stressing the importance of peace on the peninsula.
But Kim Yo-jong, the powerful sister of the North Korean leader, called the speech "disgusting" and "shameless and impudent", adding Moon "seems to be insane though he appears to be normal outwardly".
The two Koreas remain technically at war after hostilities in the Korean War ended with an armistice in 1953 but not a peace treaty.