Tony Blair's aides cautioned Mr Brown not to hire Mr McBride, who was then working as a civil servant in the Treasury, as his personal press chief.
Mr McBride, dubbed McPoison, has repeatedly insisted that the former Prime Minister knew nothing of his 'dark arts'.
But earlier this week Labour leader Ed Miliband said that he had urged Mr Brown to sack Mr McBride, in a conversation thought to have taken place in 2008.
Mr McBride's book shows that the then Chancellor also received a warning three years earlier, in the wake of that year's general election.
Mr McBride writes that Blair's No 10 wrangled with Mr Brown before signing off on the job.
He adds: "Gordon gave me a dark look during those days of wrangling with Blair over the appointment and said: "They really hate you over there. Some of the things that they accuse you of doing is just..."
"He left the thought hanging. I just shrugged."
Mr Brown has stonewalled questions over what he knew about his former spin doctor's actions.
In his book Power Trip, published yesterday, Mr McBride admits smearing Labour ministers as well as Conservative opponents.
He also reveals that Mr Brown was an ardent Scottish football fan, despite claims to the contrary, and that he had given up his 30-a-day smoking habit following the 1982 World Cup.
He also claims Mr Brown was unaware of the briefing he gave that led to infamous headlines that the former Prime Minister's favourite goal had been the one that Paul Gascoigne scored against Scotland in 1996.
Mr McBride also revealed that he had once been woken by shadow chancellor Ed Balls and while still not fully awake had mistaken him for a female bed partner.
In his book he writes that Mr Brown's famous claim to like the Arctic Monkeys came about because he was told that the alternative choice, James Blunt, was a Tory.
Tory MPs have called formally for a police investigation into whether Mr McBride broke the law by accessing Mr Brown's emails and leaking documents.
Alun Cairns has written to Metropolitan Police Commissioner Sir Bernard Hogan Howe on the subject.
l Mr McBride's publisher Iain Dale is facing questions from police after tussling with a protester as the former spin doctor gave a live television interview.