By Elizabeth Koh

South Korean prosecutors on Tuesday indicted Samsung's de facto leader Lee Jae-yong on charges alleging he manipulated stock prices and violated the country's capital-markets laws, raising the possibility that the business tycoon could return to prison.

The 52-year-old Mr. Lee, who was named along with 10 current and former Samsung executives in the prosecution's case, won't be arrested as part of the indictment. But he will have to stand trial in a Seoul district court. A trial date hasn't yet been set.

Mr. Lee, a grandson of Samsung's founder, is already on trial for a separate -- though related -- case over a 2017 bribery conviction that is in an appeals court and earlier landed him in prison.

The prosecutors' Tuesday indictment will likely unfold in courts over multiple years and the prospects of the case heading to the country's Supreme Court are particularly high, legal experts say. Major violations of South Korea's capital-markets laws call for sizable fines and can result in prison sentences of several years, those experts say.

Mr. Lee was also charged with breach of trust and violating auditing laws.

A Samsung spokesman declined to comment on the case. After Tuesday's indictment, lawyers for Mr. Lee accused investigators of targeting him and said in a statement that "there is nothing new worth refuting."

"The prosecution, which is against the will of the people and disregards the reasonable judgment of the judiciary, is not only against the legal balance but also undermines the public's trust in the prosecution," the statement said.

The case brought Tuesday revolves around the 2015 merger of two Samsung affiliates -- Cheil Industries Inc. and Samsung C&T Corp., which prosecutors have said strengthened Mr. Lee's control over parts of the family-led empire. Investigators had focused on perceived irregularities in Cheil's ownership stake in Samsung Biologics Co. before the deal went through.

In 2018, South Korea's Financial Services Commission said Samsung Biologics deliberately breached accounting rules in a move that encouraged the merger by inflating Cheil's financials and referred the matter to prosecutors. Prosecutors have alleged Mr. Lee was involved in orchestrating accounting malpractice. Samsung has rejected any allegations of wrongdoing.

Over the past several months, prosecutors conducted more than 50 search-and-seizure requests and summoned more than 400 Samsung employees and executives for questioning. They also attempted to arrest Mr. Lee in June, though a district court blocked that move.

The decision to press forward with an indictment was an unusual move by South Korean prosecutors after a panel, made up of outside experts on legal and other matters, recommended the case focused on the merger be dropped in June. The panel, formed in 2018 to review high-profile cases, was convened at Mr. Lee's request to weigh in on the legitimacy of the probe. It was the first time that prosecutors ignored the panel's guidance, though it has no binding power.

Samsung sought several times to neutralize its legal challenges, heeding a judge's recommendation in the separate bribery case to create a compliance committee and apologize to the public. In an apology earlier this year, Mr. Lee vowed he wouldn't pass control of the company to his children and that the company would remedy other shortcomings, such as discouraging unions.

Mr. Lee is formally the vice chairman of Samsung, though he has run the conglomerate since his father, Samsung Chairman Lee Kun-hee, became incapacitated after a heart attack in 2014. All key decisions and investments require a signoff from the younger Mr. Lee, who goes by "Jay Y." in the West.

Mr. Lee has spent nearly the past four years mired in political and legal scandals, largely tied to the 2015 merger that consolidated his ownership stake and tightened his grip on the conglomerate.

Mr. Lee was first indicted in 2017 on charges of bribery, embezzlement and perjury, when prosecutors asserted that the company had paid a friend of South Korea's then-President Park Geun-hye to secure government support for a merger between the two Samsung affiliates. South Korea's national pension fund cast a decisive vote in support of the merger.

Mr. Lee has denied the charges. He was sentenced to five years in prison and spent a year behind bars in 2017 and 2018. His sentence was later suspended and he was freed from prison. Then last year, South Korea's Supreme Court overturned the lower court's decision and remanded the case for retrial.

Write to Elizabeth Koh at Elizabeth.Koh@wsj.com