The anti-graft agency said Muhyiddin, 75, will face charges Friday related to alleged abuse and money laundering linked to government projects awarded under his rule.
Muhyiddin Yassin resigned on Monday after months of bitter infighting in his coalition, and with public anger growing over a worsening coronavirus outbreak.
Muhyiddin, who came to power in March 2020, will remain as caretaker until a new premier is appointed, the palace said.
The deal is expected to cover 6.4 million Malaysians, or 20 percent of the population, with another 10 percent to be covered under Malaysia's participation in the global COVAX facility, backed by the World Health Organization.
Muhyiddin Yassin is facing a premiership challenge from opposition leader Anwar Ibrahim, who last week met Malaysia's king in a bid to prove he has majority support from lawmakers, including from among government turncoats, to form a new government.
Muhyiddin's inauguration went ahead on March 1 morning despite a last-minute bid by Mahathir and his allies to prove that the veteran politician had enough support to return as the PM