Recent electoral wins and a gradual recovery in the economy have allowed Najib to sack more critics and reshuffle his cabinet, bringing in loyalists ahead of general polls that may be held as early as next year.
Shafie Apdal, who as a vice-president was the fifth-most senior leader of the United Malay National Organization (UMNO), resigned two weeks after two other senior leaders were sacked by the party over their criticism of Najib's handling of the 1Malaysia Development Berhad (1MDB) scandal.
"Justice is not being done. There is no justice in the way UMNO is being run," Shafie said on Monday at a rally in his home constituency of Semporna, a ruling party stronghold in the Borneo state of Sabah.
The rally was telecast on social media.
Shafie does not hold any post in government.
Najib has a tight grip over UMNO. He emerged stronger last month as the party's supreme council sacked deputy president Muhyiddin Yassin and Mukhriz Mahathir, the son of former prime minister Mahathir Mohamad. It also suspended Shafie, pending investigations into his conduct by the disciplinary board.
All three leaders have been sharp critics of Najib, calling for his resignation following the allegations of graft and mismanagement at 1MDB.
But the sackings and Shafie's suspension sparked an internal revolt, with local UMNO leaders in Semporna resigning en-bloc in protest.
Earlier on Monday, Shahruddin Md Salleh, an UMNO state legislator from Muhyiddin's home state of Johor, quit all his party posts.
Najib, who chaired the advisory board of 1MDB, has faced intense pressure following revelations that $681 million had been deposited into his personal account. Najib has denied any wrongdoing.
Malaysia's UMNO-dominated ruling coalition, Barisan Nasional, coasted to victory in two by-elections earlier this month, defying a political movement led by Mahathir who has sought to turn voters against Najib.
The wins, along with a landslide win in the Borneo state of Sarawak last month, prompted some political experts to believe Najib may call snap polls.
Najib has dismissed the rumours, stressing that any decision to call for national polls will "not be governed by by-elections".