With Chelsea having a bid for the England international rejected, the boss hinted a over-long transfer tussle may disrupt David Moyes' preparations.
The Blues had an opening offer for the striker immediately rejected last Tuesday and are expected to return with an improved bid.
Mourinho suggested a long transfer saga could affect the "balance" of a team very close to the start of the season, or even after the new campaign has begun.
"It depends on the philosophy of each one," Mourinho told reporters at a press conference in Jakarta. "The sooner you have the players the better. You know the squad you have, you know what you have to work with, you have time for that.
"But, yes, he [Moyes] is right. The market is open until September 2 and many clubs are waiting to the last moment to make their decisions, and those decisions affect a number of other clubs. The one who sells has to go and buy, then they have to buy to replace, so no club is safe. Until the last minute, a club can go there and 'steal' a player. I don't mean steal a player, but steal the balance that a manager has when he's working with a team."
Mourinho, though, denies he is playing "mind games" with Moyes over Rooney.
"If to say my colleague in United is a great coach, deserves success, deserves time to work, didn't win trophies at Everton because it's difficult to win trophies there, if that is playing mind games, what would you say if I spoke bad about him?" the Chelsea boss asked.