Anderson was full of praise for his first England captain, Nasser Hussain, but felt Vaughan lacked the ability to talk to his team as individuals and left him feeling "alone and isolated" when he needed support.
In an excerpt of his autobiography, which was published in the Mail on Sunday, Anderson said of Hussain: "Our relationship was good on and off the field. The same could be said of my relationship with Michael Vaughan, captain during my early England years, since his retirement. Unfortunately, despite our cordiality now, I didn't enjoy Vaughan as a captain."
He went on: "As a young fast bowler, you need to know that your captain has his arm around your shoulder, if not physically, then metaphorically. Unfortunately, that is not something I ever felt playing under Vaughan. I actually felt alone and isolated when I most needed support.
"Prime example of that was my recall for the fourth Test against South Africa at the Wanderers in 2005. I had spent the first three Tests on tour out of favour. My tour was one big net, and because I had been so far removed from selection, I wasn't even thinking about playing.
"When preferred to Simon Jones, I was underprepared. It was five months since my last first-class action. I didn't bowl very well. Although I started okay as first change, it wasn't long before I began dragging the ball down short and wide. I got clattered everywhere and was soon shot of confidence.
"Vaughan asked: 'What's up, mate? Radar gone?'
"'Yeah, I think it has,' I said, desperate for some backing. All I received was a pat between the shoulder blades and an instruction to 'keep going'."
Anderson, 30, continued: "A good captain should know how to talk to his team as individuals. I don't think Vaughan ever had that in him - a major reason I've not held him in as high regard as others have.
"He was not as good a captain as others made out. He was captain of a truly great team in 2005."