Abuse of power and breach of trust charges carry a maximum penalty of 20 years in prison for each count.
In a packed courtroom, the three new charges were read out to Mr Najib.
Last month, Najib was arrested and charged with abuse of power and criminal breach of trust related to an alleged transfer of RM42 million (S$14 million) into his personal bank account from SRC International, a former unit of 1MDB.
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The then attorney general - who had ties to Najib's party - cleared the leader of wrongdoing, and said that the money had been a donation from the Saudi royal family.
Najib, 65, pleaded not guilty before High Court judge Datuk Azman Abdullah.
The multiple charges filed against him in July were also connected to SRC International. He has pleaded not guilty to those charges and was released after posting bail, but his passport was held.
Tan Sri Irwan was removed from his post and that of 1MDB chairman after Najib was ousted.
Najib and his allies are accused of plundering billions of dollars from 1MDB to buy everything from USA real estate to artworks.
SRC has been the initial focus of Malaysian investigators as all the suspicious transactions involving it went through Malaysian entities, unlike other 1MDB-related transactions that went through foreign banks and companies.
Lawsuits filed in United States courts by the Department of Justice allege that an estimated $4.5bn was misappropriated from 1MDB by high-level officials of the fund and their associates.
On Tuesday, a luxury yacht that was allegedly procured using stolen money from 1MDB was returned to the Malaysian government.