Both players were reportedly among Great Britain coach Stuart Pearce's provisional list of 80 players last week, with United set to be the hardest hit.
With Javier Hernandez and David de Gea also set to be named for Mexico and Spain respectively, Ferguson could be left short-handed with the Olympic tournament ending just a week before the new Premier League season.
"It's ridiculous, utter chaos," he is quoted as saying in various newspapers.
"I have no idea how badly other clubs are affected but I would imagine Tottenham will have a few, like Gareth Bale.
Ferguson claimed that he had agreed with Pearce that none of the players that appear at this summer's European Championship would be a part of his Olympic squad.
Pearce is not due to name his final squad until after Euro 2012, when Rooney could play just one game due to his suspension from England's opening two group fixtures.
Pearce is allowed to select three over-age players in a squad otherwise consisting of players under the age of 23.
"We have agreed that any player who boards the plane to the European Championship in Poland and Ukraine will not be considered for selection to Team GB," Ferguson said.
"It's a sensible football decision when you consider the demands on players, and it now leaves no room for doubt for players and their clubs about next summer and the two major tournaments."