The United boss has slammed the treatment of the 'trusting' 27-year-old, and urged him to be less cooperative with English football's governing body
Rooney, who has been the subject of intense speculation following his omission from United's starting XI against Real Madrid on Tuesday, has often participated in press conferences, under instruction from the FA, when on England duty.
Ferguson is adamant that his striker should not be so cooperative with the FA, particularly as the Scot feels that they punish the England international much more harshly than they would other players over disciplinary matters.
"I spoke to Wayne [Rooney] and told him he will probably have to go through a bit of s***, that's the name of the game. I keep telling him he's too trusting. I told him: 'I don't know why you do it with the FA'," he told reporters.
"He does things every time he goes down there [with England]. He should not be doing anything with them. They've not helped him one bit.
"Every time he does anything [commits an on-field offence] they punish him more than anyone in the game. He should be realising that. He shouldn't have to do anything for the FA. They force him to do it."
The Red Devils boss also insisted that there are no issues between himself and Rooney, citing Danny Welbeck's ability as the reason for Rooney's absence from the starting XI against Real Madrid, rather than any fault on the 27-year-old's part.
"There's no issues at all, it's not about one person. The issue was that [Danny] Welbeck was better at that job against people robbing him of the ball," he continued.
"He's very good at that, Welbeck – the best we've got."