Sulley Muntari handed Portsmouth a shock FA Cup quarter-final win from the penalty spot to secure his side's place in the Wembley semis.
United wasted more than enough chances to win the match but manager Ferguson chose to vent his fury at ref Martin Atkinson and took at swipe at Keith Hackett, who is in charge of officials.
Ferguson felt United had a blatant penalty denied when Cristiano Ronaldo was blocked by Sylvain Distin.
"It's absolutely ridiculous," said Ferguson, whose side were denied the chance to repeat their 1999 Treble success.
"I cannot explain it. Managers get sacked because of things like that and he's going to referee a game next week."
He added: "He (Hackett) is not doing his job properly and he needs to be assessed.
"I'm assessed as a manager, players are assessed, referees should be assessed properly by the right people. That performance today should not be accepted by our game."
Ferguson's assessment was echoed by winger Ronaldo who claimed he is "scared" at not being given enough protection and revealed he may change his style of play.
He said: "The referee today was unbelievable. After five minutes, there had been three fouls - but he didn't give any cards.
"Then I do not get the penalty. It's very disappointing.
"He [Distin] didn't try to take the ball; he came straight to me, and when this happens it's difficult to play football. It's a joke.
"This is the best league in the world. But I'm scared sometimes because some players do unbelievable fouls, and the referee protects the defender - not the skilled players.
"I'm thinking a lot about changing my game, because this happens. They don't give penalties, don't give yellows, don't give reds - it's difficult to play like that."
He said: "Distin is strong and used his body properly. I would have been disappointed if a penalty had been given."