He was already being held at a detention centre after appearing in court Thursday as judges deliberated whether to issue an arrest warrant.
The move reverses a decision from last month where the Seoul Central District Court in South Korea rejected a request for an arrest warrant for Lee, Samsung's 48-year-old vice chairman.
The heir of South Korean company Samsung has been arrested as part of an investigation into corruption and influence-peddling that caused President Park Geun-hye to be impeached.
A decision on whether to issue the arrest warrant will likely be announced early Friday morning. If arrested, Lee would join several close presidential aides awaiting trial behind bars in connection with the scandal.
Park has been stripped of her powers while the Constitutional Court decides whether to uphold her impeachment.
Lee admitted that Samsung transferred funds to a company and foundations controlled by Choi Soon-sil, President Park's secretive friend, but denied allegations that he expected to win any government favors.
They are also investigating Lee on allegations of embezzlement of Samsung funds, hiding assets overseas and lying under oath during a parliamentary hearing.
According to Bloomberg the de facto head of Samsung, known professionally as Jay Y. Lee, had been summoned to court as of 6 AM local time on February 17.
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.
After the prosecutor's first attempt to arrest Lee was rejected by a court on January 19 due to lack of evidence, the billionaire heir was called in again for 15 hours of questioning on Monday as investigators sought more information.
Industry observers said Samsung may be affected by US anti-corruption laws after Lee was arrested on charges of bribery.
Prosecutors accuse Lee in his capacity as the head of South Korea's largest conglomerate of pledging 43 billion won ($37.7 million) to a business and organisations backed by Choi in exchange for support of a 2015 merger of two Samsung companies.
Korea's National Pension Service, a $452 billion fund with money from 22 million citizens, was the largest investor in Samsung C&T and voted in favor of the merger, playing a key role in its narrow approval.
The merger was opposed by many minority shareholders, who said the deal would hurt them while unfairly benefiting Lee and other members of Samsung's founding family.
Lee Jae-yong took over the Samsung conglomerate in October 2016, after his father, Lee Kun-hee, suffered a heart attack in May 2014, which still keeps him hospitalised and unable to communicate. After his latest conviction in 2008, he was pardoned a year later by the president, who said he would help South Korea's bid to host the 2018 Winter Olympics.