The striker, 31, made only 12 Premier League appearances for United in 2011-12, moving to Fulham last week.
"I said goodbye to the people who deserve it, I couldn't say goodbye to Ferguson," said the Bulgarian.
"I know he's the boss but he has lost, to some extent, my respect because of the way he treated me."
Berbatov moved to Old Trafford from Tottenham for £30.75m in 2008 and was the Premier League's top scorer in 2010-11.
But he was left out of United's squad for the 2011 Champions League final against Barcelona and then featured only fleetingly last season.
"I don't think I deserved such treatment at United, not playing in the last year," he told reporters in Sofia.
"I went probably 15 times to ask the coach if he needed me. Every time I was told that I'm an important player and should not leave but then again I was not in the team. Maybe I should have gone when he left me out of the squad for the Champions League final."
Berbatov's agent Emil Danchev also revealed that Tottenham had made a last-ditch attempt to re-sign their former player.