The billionaire, who is the vice chairman at Samsung Electronics, has been accused of bribery in a case linked to the scandal that led to the impeachment of the country’s president Park Geun-hye, the BBC said.
Samsung has been accused of giving donations worth 41bn won (£29m) to non-profit organisations in exchange for government support for the company’s restructuring plans.
The non-profit organisations which were awarded by Lee were operated by Choi Soon-sil, a friend of the South Korean president.
Lee had been questioned in January by prosecutors, who did not arrest him at the time for lack of evidence. He was then questioned again this week and arrested on Friday.
According to BBC correspondents in Asia, the court said that he was being arrested “in light of a newly added criminal charge and new evidence”. Prosecutors have now 20 days to file formal charges.
Lee is expected to take control of Samsung once his father, Lee Kun-hee steps down. However, he has been acting as Samsung chief since his father had a heart attack in 2014.
Kun-hee was also charged with bribery by the then-president Roh Tae-Woo and was given a two-year suspended sentence in 1996.
In 2007, he was charged with tax evasion and other charges and sentenced to three years in jail, suspended for five years. One year later, he was acquitted.
Samsung has been contacted for comment.