In his autobiography 'Taking the Mickey - The Inside Story' to be released Monday, Arthur writes that Ntini accused him and captain Graeme Smith of racism after he was axed from the side due to indifferent form at the start of 2008-09 season.
"Everybody, especially senior players, is upset when they are dropped, but I was desperately disappointed when Makhaya started telling influential administrators that Graeme Smith and I did not want black players in the team," Arthur wrote.
Ntini, who retired from international cricket earlier this week, became the first black cricketer to play for South Africa after the end of apartheid.
Arthur, who considered Ntini for team and always believed in picking a player on merit and not colour, writes that he was taken aback at Ntini's behaviour.
"I was flabbergasted and I felt my anger rise (on Ntini accusing him of racism after being dropped)," wrote Arthur.
"At the time, I thought how ashamed Makkie (Ntini) would be in the years to come when he reflected on the way he had behaved."
These revelations come at a time when another South African cricketer, Herschelle Gibbs, in his book accuses Arthur and Smith of being too powerful in the team.
Gibbs also narrates in his book 'To the Point' on how he along with fellow players indulged in sex orgies, alcohol binges and smoking pots during many foreign tours.