The 69-year-old failed to win any trophies in his first three years with the Red Devils and was rumoured to be close to the sack before an FA Cup victory over Nottingham Forest in 1990, with United going on to win the trophy.
However, Charlton has refuted those suggestions and insists he always had the board's full backing.
"There wasn't one board meeting where it was brought up. Never," Charlton told the Sunday Telegraph. "He knew what he was doing.
"You could see the growth of the young players, and we knew it was only a matter of being patient. And we were patient, because we knew that he was still the man for the job.
"We ran the club, but the playing side was left to him. He was a genius. He is a genius."