The 28-year-old striker has featured in all but one of United's Premier League fixtures in the 2013-14 campaign, and started both of England's most recent friendlies against Chile and Germany respectively.
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"I expected him to play in both games, but maybe for not quite as long," the United manager said. "I was hoping we could have got Wayne some time off with England but obviously Roy has to pick his teams and the games were important for him, I respect that.
"But somewhere along the line I’ll probably need to give Wayne a breather. I'll need to try to look after him as we go along. It might be the next England game against Denmark in March but I know Wayne and he will want to play.
"I've probably got another 25-30 games before that March game so it's not me saying to England give him a break in March – I think I probably need to look after him somewhere in the next two months."
Rooney, meanwhile, has hit back at suggestions that he is in better shape now than in previous campaigns, with Sir Alex Ferguson having stated in his autobiography that Rooney's great qualities could be "swallowed up by a lack of fitness".
"I'm just saying it's [Rooney's fitness] the same as last season. But, obviously, it's been noticed this season. That's all," he said. "Every player gets the stats from every training session and every game. The stats are pinned up around the training ground every day and after every game you always get your stats, and it's the same system with England at Wembley.
"It's something which you can monitor in terms of how much work you are doing and sometimes you do need a bit of a rest, so that’s what we do.
"I think it's something we see every day, the coaches give us every day and they have done for years. So it's important to know how much running you’re doing and it’s important to know when you need a rest at times. That's why we look at them."