The finance ministry said Wednesday that it filed a complaint against a former junior official for leaking secrets, which he claimed was whistleblowing aimed at serving the interest of the public.
The Ministry of Economy and Finance took legal action against Shin Jae-min on charges of divulging official secrets and violating the public records management act.
The prosecution did not immediately say when it will begin its probe into the case.
The ministry's move came after the 33-year-old claimed that the ministry tried to issue deficit-covering bonds worth 4 trillion won ($3.58 billion) in late 2017 under pressure from the presidential office.
Shin -- who worked at the ministry's treasury department -- claimed in several online postings and YouTube clips that the move was apparently aimed at increasing government debts for the fiscal year 2017 to make the former Park Geun-hye administration look bad.
In April, Park was sentenced to 24 years in prison and fined 18 billion won in a ruling on a massive corruption case that led to her removal from office in March 2017.
President Moon Jae-in took office in May 2017.
Shin has said he decided to blow the whistle because no one was held responsible for confusing the bond market and he was prepared to take legal responsibility for his leak.
"I don't think a person who blew a whistle for the public interest should hide and be buried in society," Shin said in a news conference at a building in southern Seoul.
Shin said he will cooperate in good faith with the prosecution's probe.
Under the law, current and former government officials can face up to two years in prison if convicted on charges of leaking official secrets.
Shin, who worked at the ministry for four years, said he was not politically motivated and he just hoped that his actions would improve the country's bureaucratic system.
Deficit-covering bonds are issued when government spending exceeds tax revenue, but tax revenue was expected to surpass spending when then-finance minister Kim Dong-yeon ordered an additional bond issuance, Shin claimed.
The ministry scrapped a government bond buyback in December 2017, just one day before the planned purchase.
The ministry said it made a final decision not to issue additional debt-covering bond after consultations with the presidential office, noting there was no "forced order" from above.
Shin has also said that the presidential office made a failed attempt to replace the CEO of KT&G Corp, a claim rejected by the ministry.
In March, South Korea's state-run Industrial Bank of Korea called for a CEO change at KT&G during a shareholders meeting, but it was voted down, according to market sources.
Foreign investors and the Industrial Bank of Korea had 53.3 percent and 6.9 percent stakes in KT&G as of the end of 2018, respectively.