Ferguson is concerned that Rooney has suffered broken bones three times in his career.
Ferguson revealed that the England striker is ahead of schedule in his latest recovery following his injury against Reading and could be ready to play in three weeks.
But Ferguson has told his players to wear reinforced soles, while club medics are also looking to alter Rooney's running style to ease the pressure on his body.
Ferguson told the Sunday Mirror: "We have looked into how the injury occurred and I don't think it had anything to do with his boots, but I have spoken with Nike and gone across all the issues with them.
"Nike aren't slow in addressing such things because they don't want their best client and our best player sidelined every year because he's broken a bone. So Nike have been efficient in that respect and are going through certain solutions."