Ferdinand was selected for England's recent World Cup qualifiers against San Marino and Montenegro, only to withdraw due to an 'intricate and pre-planned' training regime.
The 34-year-old has since been the victim of abuse from England fans.
"He did the right thing to go down and see Roy," said Ferguson. "I encouraged him to go down and do it face to face."
Ferguson continued: "He needed to explain how we handle him now and how he prepares for games.
"I think Roy appreciated that."
The United boss also said he had no issue over Ferdinand's trip to Qatar, which caused such consternation among the England fans.
"I was only catching up on a couple of things over the last couple of days and to be honest it doesn't bother me one bit," he said. "They had the weekend off and players are entitled to do what they want.
"They trained all last week and we gave them Friday, Saturday and Sunday off. He has his own choice with these things.""
Has Fergie's explanation ended the issue? Give us your shout below...