SEOUL, South Korea — A former cabinet minister was arrested Saturday on charges that he illegally pressured the national pension fund to approve a merger between two Samsung subsidiaries, a deal that helped ensure that control of South Korea’s most powerful conglomerate passed from its chairman to his son.

Prosecutors have accused the former official, Moon Hyung-pyo, of ordering South Korea’s National Pension Service to cast a crucial vote in favor of the merger between Samsung C&T and Cheil Industries in July of 2015, when Mr. Moon was the health and welfare minister. Mr. Moon is now chairman of the pension fund, the world’s third largest, which is overseen by the Health Ministry.

Mr. Moon denied the accusation at a parliamentary hearing on Nov. 30. But on Saturday, a court granted a special prosecutor a warrant to arrest him on charges of abusing power and interfering with what was supposed to be the pension fund’s independent investment decision.

A conviction of Mr. Moon on the charges would raise serious questions about the legitimacy of the $8 billion merger, which helped Samsung’s vice chairman, Jay Y. Lee, tighten his control over the business that his father and grandfather built into South Korea’s biggest, most lucrative chaebol, or family-controlled conglomerate. Mr. Lee’s father, Lee Kun-hee, is Samsung’s chairman but has been incapacitated by health problems.