The officer, identified by local media only as Lim, was a 20-year cyber-security veteran of the country's National Intelligence Service (NIS) and ran the department that used the software, according to reports.
He was found dead on Saturday in a car south east of Seoul. Burnt coal was found in the car and an autopsy conducted a day after his death on Saturday found he died of asphyxiation, according to reports. Burning charcoal in a confined space is a relatively common method of committing suicide in South Korea and Japan.
Dealings between Hacking Team and the NIS were made public when a cache of the company's emails was recently published on the Internet.
The software, called "Remote Control System," allows users to target the computer or cellphones of people and install a spyware application that gives the user access to the target's communications. It is said to be resistant to attempts at removal and the leaked emails show Hacking Team sold and demonstrated the system to law enforcement agencies across the world.
In South Korea, the revelation has been politically explosive.
A distrust of the spy agency exists in the country after a string of scandals and allegations that it spied on citizens and attempted to influence public opinion in the run up to the 2012 national election.
The NIS bought the software in 2012.
As part of the Hacking Team leak, a log file of IP addresses was published that is said to include some at Korea Telecom, national broadcaster KBS, Seoul National University and major portal and instant messaging service Daum Kakao. One of the leaked emails notes that Hacking Team's South Korean customers are interested in gaining access to Kakao chat.
But Lim, in his suicide note, denied the Hacking Team software was used to spy on civilians.
"There was no spying on locals in relation to elections at all," the note said, according to Yonhap News.
Lim had been found to have deleted information related to use of the software, and the note called that decision "a mistake."
"I decided the NIS was more important than whatever impact [my action] would cause, and so I deleted information that created misunderstandings about our counter-terrorism and covert operations on North Korea," the note said, according to Yonhap. "It was a mistake on my part. But there is nothing to be worried about over any of my actions."
The NIS had previously told South Korea's parliament that its use of the Hacking Team software was for external surveillance purposes.
Martyn Williams covers mobile telecoms, Silicon Valley and general technology breaking news for The IDG News Service. Follow Martyn on Twitter at @martyn_williams. Martyn's e-mail address is martyn_williams@idg.com