Lee was arrested over his alleged role in the corruption scandal involving impeached President Park Geun-hye.
A Constitutional Court ruling on whether to uphold the impeachment, which would result in South Korea’s first democratically elected leader being thrown out of office, is expected next month.
Lee Kyu-chul, a spokesman for the special prosecutor said the Samsung Five will face charges including bribery, embezzlement and hiding assets overseas.
Lee will also be charged with committing perjury before parliament, he added.
The other executives to be charged are Samsung Group vice chairman Choi Gee-sung, president Chang Choong-ki and Samsung Electronics president Park Sang-jin and executive vice president Hwang Sung-soo, the spokesman said.
A Samsung Group spokeswoman declined to comment on the charges.
Lee, the spokesman, said the case against President Park would be handed over to regular prosecutors with Park remaining a suspect, while signalling other conglomerates may also become involved in the investigation.
Park was impeached by parliament in December after accusations that she colluded with long-time friend Choi Soon-sil to pressure big businesses, including Samsung, to donate to two foundations set up to back the president’s policy initiatives.
The special prosecutor’s office will make an official announcement regarding the conclusion of its investigation on March 6.