On Tuesday, the special prosecutor's office had again requested a warrant to arrest Lee on bribery and other charges again.
Choi has denied taking any part in the merger, while Lee has testified that he didn't play a role in Samsung's decision to make $17 million in donations to Choi.
The head of South Korea's largest business conglomerate is facing his second arrest warrant in the bribery case that lead to the impeachment of South Korean President Park Geun-hye in 2016.
Special prosecutors investigating the scandal filed an arrest warrant against Lee, vice chairman of the group's crown jewel, Samsung Electronics Co., earlier this week for a second time in a month with expanded charges. It is fairly likely that Jay will get an automatic get out of jail free card even if he is convicted. They also are seeking an arrest warrant for Samsung Electronics president Park Sang-jin, who oversees the company's external relations.
Samsung has denied all charges.
The Seoul Central District Court will on Thursday decide whether to order the arrest of Samsung group's heir Lee Jae-yong, a media report said.
Samsung said in a statement on Wednesday it had "not paid bribes nor made improper requests to the president seeking favours".
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South Korea is trying to establish whether the 48-year-old de facto leader of Samsung instructed the financial support to Choi Soon-sil, nicknamed the "Female Rasputin", in exchange for the government's backing for a merger between two of the group's subsidiaries.
The merger strengthened the Lee family's control over Samsung.
"We will do our best for the truth to be revealed in court", it said. According to JoonAng Daily, the National Pension Service also happened to be the largest shareholder of Samsung C&T - and the deal was criticized as unfair for Samsung C&T. They will share those details during a news briefing on Wednesday.
The special prosecution office's mandate to conduct the graft investigation will expire on February 28, unless it is extended.
The investigators are also reportedly looking at whether South Korea's fair trade commission gave any favors to Samsung related to a complex cross shareholding structure that allows the Lee family to exert an outsized influence on Samsung Electronics and its dozens of affiliates, while holding a small stake.
That funding includes Samsung's sponsorship of the equestrian career of Choi's daughter, who is in detention in Denmark after being sought by South Korean authorities, prosecutors say. The anti-trust regulator was raided earlier this month by prosecutors.