Mr Hwang, 87, once a close confidant of North Korean leader Kim Jong-il, defected to the South in 1997.
Pyongyang’s official government website had recently threatened him with death.
The alleged plot to kill Mr Hwang was uncovered when the two men, named by the Yonhap news agency as Kim and Tong, crossed into South Korea from Thailand earlier this year, posing as defectors themselves.
They were questioned by South Korean officials during the debriefing sessions that await all North Korean refugees who make it to Seoul.
A unnamed senior official at Seoul Central District Prosecutors’ Office told reporters they had said their orders were to “slit the betrayer’s throat”, the Associated Press news agency reports.