Samsung Electronics' share fell 1.25 percent the same day Lee was questioned by authorities. It had been hoped that Lee Jae-yong's taking over the reins from his father would provide some much needed stability.
Lee's arrest will cause an immediate void in the Samsung Group's leadership, a awful scenario that the company has been bracing for a while.
"We will do our best to ensure that the truth is revealed in future court proceedings", the group said in a statement.
The Seoul court said it would hold a hearing on the arrest warrants request at (0130 GMT) on Thursday.
If the court grants the arrest warrant, Lee faces the prospect of months in jail while awaiting trial. If Lee is arrested, it would deal a serious blow to Samsung, the world's biggest maker of smartphones, memory chips and flat-screen televisions, potentially hampering strategic decision-making, such as new investments and acquisitions.
Last year 48-year-old Lee Jae-yong took over the running of the company from his father Lee Kun-hee, who suffered a heart attack in 2014 but remains leader of the Samsung Group.
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But prosecutors on Tuesday made a second bid, saying they had collected more evidence in recent weeks. Analysts, however, stated that the incident will not affect Samsung's market performance. Lee has denied wrongdoing and the decision might not be released until Friday.
In January, Samsung heir Jay Y. Lee was accused of bribing South Korean President Park Guen-hye; now he has been arrested.
Samsung was the single biggest donor to the foundations. Samsung also transferred millions of euros to Choi's company in Germany that financed the equestrian training of Choi's daughter and funded a winter sports center operated by Choi's niece. The court rejected the prosecutor's request to arrest Samsung Electronics President Park Sang-Jin.
Prosecutors also allege that Samsung sought political favours in the controversial 2015 merger of its de facto holding company Cheil Industries Inc with Samsung C&T Corp, its construction arm.
Samsung is South Korea's largest business group and its revenue is equivalent to about a fifth of the country's GDP.
The president and prosecutors have still not agreed on a schedule for her questioning, but the telephone records for Park and Choi could give weight to the prosecutors' argument.