Officers using drones and sniffer dogs found Mayor Park Won-soon's body at Mt Bugak in northern Seoul shortly after midnight following a search involving hundreds of police, the Seoul Metropolitan Police Agency said.
There was no sign of foul play and police did not give a cause of death.
The apparent suicide came after one of Park's former secretaries filed a complaint on Wednesday alleging the 64-year-old had sexually harassed her, the Yonhap news agency reported.
Police confirmed a criminal complaint had been made against Park but did not elaborate on the nature of the allegations.
"I apologize to everyone," Park wrote in a note left on his desk and released by the city government with the permission of his family.
"I thank everyone who was with me in my lifetime. I am so sorry to my family, to whom I have only caused pain."
The note did not mention any allegations.
A representative for Park's family issued a statement on their behalf saying it was time to let him go and urging people to avoid spreading "groundless statements."
"If acts of defaming him continue irrespective of the truth, we will sternly respond with legal action," said Moon Mi-ran, who formerly served as deputy mayor under Park.
Many residents of Seoul, a city of nearly 10 million people, expressed shock over the sudden death of the former activist, women's rights advocate and lawyer who many saw as a potential presidential candidate.
"I feel sorry, but apart from that there needed to be a clear explanation on the sexual harassment," Jeon Sung-jae, an office worker, commented on Park's death amid the reported allegations.
“SHOCKING AND REGRETFUL”
Park's daughter reported him missing at 5:17 p.m. (0817 GMT) on Thursday, police said. He had left the mayor's official residence at around 10:40 a.m. on Thursday, wearing a black hat and a backpack, having canceled meetings for the day.
His body was taken to Seoul National University Hospital, where five days of funeral events were expected to begin.
Leading lawmakers of both ruling and opposition parties expressed condolences, as did the U.S. ambassador to South Korea, Harry Harris.
Ruling party chief Lee Hae-chan said Park's death was “shocking and regretful,” recalling him as an old friend who fought together for democracy during a dictatorship in 1980s.
As Seoul mayor since 2011, Park was instrumental in its response to the coronavirus pandemic. He also played a vocal role in massive candlelight demonstrations that contributed to the ousting of former President Park Geun-hye in 2017.
An outspoken advocate of women's rights and gender equality, he was seen as a potential presidential hopeful for the liberals in elections scheduled for 2022.
As a lawyer in the 1990s, he won one of South Korea's earliest cases on sexual harassment, and strongly advocated for the cause of "comfort women" who were forced to work in Japan's wartime military brothels before and during World War Two.
Park also praised women for their courage after a series of women accused powerful politicians and policymakers of sexual wrongdoings amid the #MeToo movement in 2018.Oh Keo-don, the former mayor of Busan, South Korea's second-largest city, and another major player in liberal politics, stepped down in April after acknowledging unnecessary physical contact with a female staffer.