Mr. Lee, 48, a vice chairman of Samsung, has been running the company since his father had a heart attack in 2014. His indictment comes after a challenging period for the company, which issued a global recall of its Galaxy Note 7 smartphones, the most ambitious product launched under his leadership, because they were prone to catching fire.

The elder Mr. Lee was convicted of bribery and tax evasion twice but never spent a day in jail. Each time, he was pardoned by the president and returned to the company. At least six of the nation’s top 10 chaebol — which generate revenue equivalent to more than 80 percent of gross domestic product — are led by men once convicted of white-collar crimes.

Ms. Park was identified as a criminal accomplice in November, when state prosecutors indicted Ms. Choi on charges of extorting tens of millions of dollars from Samsung and other chaebol by leveraging her connections with the president. But she was protected from indictment while in office.

On Tuesday, the special prosecutor, Park Young-soo, added a bribery charge to the case against Ms. Choi, who is already on trial. He said Ms. Park could also face bribery and extortion charges once she leaves office. Ms. Park denies any wrongdoing, saying the money from Samsung was part of “donations” that businesses provided to two foundations that prosecutors said were controlled by Ms. Choi.

Ms. Park’s presidential powers have been suspended since the National Assembly impeached her in December. The Constitutional Court is expected to rule in the coming weeks on whether Ms. Park should be formally ousted or reinstated and allowed to finish her five-year term, which ends next February.

In the current scandal, Samsung was accused of making payments to Ms. Choi in exchange for a crucial vote by the government-controlled National Pension Service to support the 2015 merger of two Samsung affiliates. The special prosecutor says Ms. Park ordered the pension fund to support the merger on Mr. Lee’s behalf.

The merger caused a loss of at least $123 million for the national pension fund, which held large stakes in the two affiliates, but it increased the stock value of the Lee family by at least $758 million, the prosecutor said.

The four executives under Mr. Lee who were also indicted belonged to Samsung Electronics or to the conglomerate’s powerful, secretive Corporate Strategy Office. Critics say the office worked mainly to tighten the Lee family’s imperial control of the conglomerate and enforce the father-to-son transfer of leadership. On Tuesday, Samsung said it was disbanding the office as part of its effort to make its corporate governance more transparent.