A warrant for his arrest was issued by the Seoul Central District Court early on Friday. It was sought on Tuesday by the investigation team that is looking into the scandal, the second time that it had done so after the court in January turned down a similar request.
Lee, the deputy chairman of Samsung Electronics, became the first leader of South Korea's largest business group to be held over a criminal probe, the Yonhap news agency reported. He will face charges of bribery, embezzlement and perjury.
The investigators say that more criminal charges have been made against Lee compared to the last time it sought his arrest.
But it did not agree to grant a second warrant, for the arrest of Samsung Electronics president Park Sang-jin, on the grounds that it was difficult to recognise the need to detain him.
Lee will now have to stay at a detention centre in Uiwang, south of Seoul, where he had been awaiting the ruling.
According to Yonhap, the Samsung Group is alleged to have signed a 22 billion won (US$18.3 million) contract with a Germany-based company owned by Choi Soon-il, a confidante of Park, and her daughter, under a consulting arrangement to pay for the daughter's equestrian training.
The investigators are examining whether this contract was signed as a quid pro quo for the state-run pension fund's backing of a major 2015 merger deal between Samsung subsidiaries.
Allegations have been made that the presidential office put pressure on the state fund to back the merger in return for the alleged favours that Samsung granted Choi.
Park, meanwhile, is waiting for the Constitutional Court to decide whether to uphold the impeachment vote which took place on 8 December 2016.
The scandal and its fallout comes after a year in which Samsung had to stop production of its flagship Galaxy Note7 after numerous devices combusted. Samsung also faced issues with washing machines and had to order a recall.