Ferguson's men were involved in a controversial incident during last Sunday's Community Shield at Wembley when defender Patrice Evra went down injured but Chelsea played on and scored, with referee Chris Foy playing the advantage.
The Scot claims referees are finding it increasingly difficult to differentiate between genuine instances when the game needs to be stopped to treat injuries and when players are trying to trick them into blowing the whistle.
A further complication is that the decision to stop play is not entirely in the official's hands, with some players still opting to abide by what Ferguson calls the "unwritten rule" to kick the ball into touch when a player goes down, injured or otherwise.
Ferguson feels if players only went to ground when genuinely injured, the referee's job would be much easier.
"This unwritten rule has come into the game and opportunist players have just overdone it. They have overcooked the whole thing," he said.
"Last week Evra was through and into the last third of the pitch, the referee stops it and (Michael) Ballack gets up. It could have been a serious problem so he stopped the game.
"Then when Evra is fouled, Chelsea don't kick the ball out, the referee plays on and we lose a goal.
"It is a grey area and something has to be done about it.
"The players are killing the game. The players' unprofessionalism is killing the game. Not the referees. The problem is how much the referee can tolerate when the players lie down pretending to be injured.
"There is no doubt that this unwritten rule about players kicking the ball into touch has been exploited to ridiculous degrees now."
Ferguson added: "I spoke to my players about it and told them not to kick the ball out, that they should let the referee decide when to stop the game.
"But the players wouldn't do it. If players don't put the ball out they get stick off opposing players and opposing fans.
"If a referee stops the game twice when players go down and on the third occasion he decides to play on, he makes a rod for his own back.
"Last Sunday, Chelsea had plenty of time to kick the ball out when Patrice Evra was injured after being fouled by Michael Ballack."