The chairman of Samsung has been incapacitated since a heart attack in 2014. His son has been running the conglomerate, which has annual revenue of 270 trillion won ($229 billion). Its crown jewel, Samsung Electronics, accounts for one-fifth of all South Korean exports.

Corruption scandals in the chaebol often stem from maneuvers to transfer wealth control from one generation of the dominant family to the next, and the trouble at Samsung is no exception.

In 2009, the elder Mr. Lee was convicted of evading taxes on 4.5 trillion won ($3.8 billion) that he secretly inherited from his father, Lee Byung-chull, the founder of Samsung. The funds were kept hidden in the bank and securities accounts of Samsung executives. He was also convicted of involvement in helping his son buy stocks of a Samsung subsidiary at an illegally low price.

In the current scandal, Samsung was accused of making payments to Ms. Choi in exchange for a decision by the government-controlled National Pension Service to support a contentious 2015 merger of two Samsung affiliates. Moon Hyung-pyo, the chairman of the pension fund, was indicted on Monday on charges that he illegally pressed the fund to back that merger when he was South Korea’s health and welfare minister.

The special prosecutor said that Mr. Moon acted on behalf of Ms. Park.

The national pension fund’s support was crucial for the merger, which analysts said helped Mr. Lee inherit control of Samsung from his father. Elliott Management, an American activist hedge fund, and other investors in Samsung had campaigned to block the merger, saying that it wronged minority shareholders by grossly undervaluing the shares of one of the two Samsung companies, Samsung C&T.

Samsung issued a statement on Monday denying that it paid bribes or made “improper requests related to the merger of Samsung affiliates or the leadership transition.”

Allegations that Ms. Park helped Ms. Choi extort millions in bribes from Samsung and other companies are at the heart of the corruption scandal that led to the impeachment vote. Ms. Park’s powers have been suspended while the Constitutional Court decides whether to end her presidency.