The charges relate to the doctoring of gas emission test results on Porsche cars so as to receive local government certification between 2014 and 2015. Porsche, which is owned by the Volkswagen Group, sold 2,000 units of those models up until February 2017, according to Yonhap.
The officials were also charged with violation of environmental laws and obstruction of business in Seoul on Monday. They are not currently being held.
The indictments follow a raid of Porsche's offices in Germany last week investigating the company and three current and former employees for knowing the engines by sister brand Audi had been manipulated. A senior executive was reportedly arrested.
"We reject these allegations and will do our utmost to clear up the matter," Porsche CEO Oliver Blume told staff in a memo, seen by Reuters.
Nearly three years ago it emerged Volkswagen had rigged millions of diesel-powered cars to cheat on emissions tests around the world. The company admitted to equipping nearly 11 million cars with software that cheated the emissions tests.
South Korea has also been active in targeting misleading behaviour by Volkswagen and other automotive manufacturers.
The environment ministry last year announced it would fine BMW AG, Mercedes-Benz, and Porsche a collective $63.1 million (R762 million) for violating emissions rules.
Prosecutors have already indicted six current and former officials from BMW Korea on charges of falsifying records since 2011 and, according to Yonhap, an investigation into Mercedes-Benz is ongoing.