Seoul prosecutors have accused Lee of involvement in a company-wide operation to dismantle a union at Samsung's after-service unit between 2013 and 2016 when he was chief finance officer.
The indictment of Lee and other company officials on Thursday is another headache for the tech giant whose vice chairman Jay Y. Lee, the heir to the Samsung Group, is appealing a conviction for bribery in a scandal that led to the impeachment of South Korea's former president.
Lee Sang-hoon, who has led the board since March, is not related to the founding family.
"His status remains unchanged," a company spokeswoman said.
Ra Doo-shik, who leads a union representing more than 1,000 workers at Samsung Electronics Service, said on Friday that the indictment was encouraging.
"We are hoping that upcoming court proceedings will reveal the true picture," Ra told Reuters.
Jay Y. Lee, the de facto leader of the South Korea's biggest conglomerate, was released on a suspended sentence in February after spending nearly a year in jail. He initially received a five-year term but a higher court later reduced that by half and suspended the sentence.
(Reporting by Ju-min Park; Editing by Edwina Gibbs)