SEOUL, South Korea — A former chief justice of South Korea’s Supreme Court was arrested early Thursday on charges of conspiring with the nation’s disgraced former president to manipulate its ruling on a case that threatened to upset relations with Japan.

The ex-justice, Yang Sung-tae, 71, is the first former or sitting chief justice to be arrested on criminal charges in South Korea. He was taken into custody shortly after a court in Seoul, the capital, issued an arrest warrant early Thursday.

Mr. Yang’s arrest is expected to be followed by a formal indictment. Although Mr. Yang has vehemently denied all charges against him, prosecutors in South Korea seldom fail to indict criminal suspects they have arrested.

Mr. Yang, who served as chief justice from 2011 until 2017, is also accused of discriminating against judges considered unfriendly to his leadership and to the former and impeached president, Park Geun-hye, by influencing job postings and promotions.