Najib has now been hit with 38 charges since losing power, most of them related to allegations that he and his cronies plundered vast sums from sovereign wealth fund 1MDB.
The scandal played a major part in prompting voters to oust his coalition at elections in May after six decades in power and elect a reformist alliance headed by Mahathir Mohamad.
Najib was jointly charged in a Kuala Lumpur court with ex-senior finance ministry official, Mohamad Irwan Serigar Abdullah, with six counts of criminal breach of trust.
They denied all the charges.
The crimes involved 6.6 billion ringgit (USD 1.6 billion) of public money and allegedly took place between December, 2016 and December, 2017.
Each charge is punishable by up to 20 years in jail.
Local media reported that some of the money was used to pay debts owed by 1MDB to Abu Dhabi sovereign wealth fund IPIC.
The Malaysian fund slid into a massive debt hole as huge sums of money were allegedly stolen and used to buy everything from a super-yacht, to high-end real estate and pricey artworks.
The US Department of Justice, which is seeking to seize assets allegedly bought with looted 1MDB money in America, alleges that a total of USD 4.5 billion was misappropriated from the fund.
Another key Najib ally, former spy chief Hasanah Abdul Hamid, is expected to be charged in court later Thursday.
The former prime minister's luxury-loving wife, Rosmah Mansor, and the new leader of his party and long-time lieutenant, Ahmad Zahid Hamidi, have also been arrested and charged.