The murder case has sparked controversy as the family of the official, Lee Dae-jun, refuted claims by the administration of former President Moon Jae-in that he sought to defect to the North due to gambling debts, mental health issues and an unhappy life.
The incumbent President Yoon Suk-yeol's government has reversed that interpretation, saying there was no evidence of a defection attempt. Prosecutors also launched an investigation into Lee's death and a 2019 case in which two North Korean fishermen were deported to the isolated country against their will.
Moon's then national security advisor, Suh Hoon, faces allegations that he had ordered intelligence reports to be deleted to conceal Lee's killing and manipulated evidence to support the defection claim.
The Seoul Central District Court, following a 19-hour deliberation, granted an arrest warrant for Suh on Saturday, citing "the gravity of the issue, the status of the suspect, and the risk of evidence destruction."
Suh, who also served as a spy chief, declined to answer reporters' questions when he appeared for the deliberation, but has denied the allegations and accused the Yoon government of political retaliation.
"It is unimaginable to manipulate a case that stakes a citizen's life and honour," Suh told a news conference in October, saying he made decisions based on analyses of intelligence and circumstantial evidence.
Yoon's ruling People Power party said Moon and his aides "not only let Lee die but killed his honour by claiming his defection while treading on eggshells around (North Korean leader) Kim Jong Un's regime."
"Now only one person remains beyond the line of truth - former President Moon," People Power said in a statement.
Yoon's office did not immediately respond to a request for comment but has said prosecutors operate independently and it was not involved in their investigations.
Suh's arrest prompted debate among lawmakers over whether prosecutors would expand the investigation to seek criminal charges against Moon, who prioritised inter-Korean reconciliation until his term ended in May.
Moon has denounced the investigation as "going too far" and issued a statement this week accusing the Yoon administration of making groundless claims and politicising security issues.
Lee's brother, Lee Rae-jin, issued a statement refuting Moon's comment, saying his government failed to rescue Lee and is now bent on "wordplay". He criticised Moon for demanding evidence to show why his brother did not defect, without presenting any proof to back his own claim.
(Reporting by Hyonhee Shin; Editing by Lincoln Feast.)
By Hyonhee Shin