Ronaldo starts a three-match ban on Sunday following his red card at Portsmouth on Wednesday when he aimed a head-butt at Richard Hughes.
Although the United boss does not condone the winger's actions, he feels Ronaldo was the victim of intimidation and an apparent unwillingness by Premier League officials to clamp down on dangerous tackles.
And, unless the problem is sorted out, Ferguson fears Ronaldo could be at risk.
"There is every chance Cristiano could get a serious injury," he said.
"I don't know if there is a directive but I have noticed over the last few months, referees seem to be more tolerant of physical contact.
"A lot of late challenges have gone unpunished and on Wednesday that happened time and time again.
"I don't know whether referees have been instructed to manage these situations but to me, it is black and white.
"That does not mean players should get away with doing stupid things on the pitch but there is a concern players like Ronaldo are going to be the victims.
"Cristiano fell for a 100-year-old trick on Wednesday but it is very difficult to completely punish him or to be angry with him because some of the things that happen to him are not right."
Ferguson was particularly incensed that respected Sky Sports pundit Andy Gray claimed Reading's Dave Kitson should not have been sent off for his studs-first challenge on Patrice Evra at Old Trafford on Sunday.
Kitson had only been on the field for 37 seconds before he launched himself at Evra, drawing a stinging rebuke in the tunnel from Ruud Gullit, who felt the striker was way out of line.
However, much to Ferguson's frustration, Gray adopted a more conciliatory stance.
"It disappoints me to hear Andy Gray saying Kitson should not have been sent off," said the United boss.
"In the 1970s he was bashing into the centre-halfs and full-backs all over the place. He forgets this is 2007.
"If Patrice Evra's foot had been on the ground it would have been a very serious challenge. I know Kitson is not that kind of player but it could have killed the boy's career."
Ferguson resisted the temptation to launch another sustained attack on Wednesday's referee Steve Bennett, who also sent Ronaldo off during a stormy Manchester derby at Eastlands two years ago.
However, he did brand the Orpington official "weak" as he assessed the impact of the events at Fratton Park.
"You are not going to change Ronaldo," he said.
"He is a player who is going to attack defenders. He does it all the time.
"There is no-one better in the game at that, it is what we want to see.
"But when you have a weak referee, like Wednesday night, you are going to be suffering.
"I am not saying the red card was wrong because the minute you lift your hand or motion towards someone with your head, you know the result.
"But the guy grabbed him round the neck prior to that. I have seen that quite clearly.
"The referee is standing there and does nothing."