Mourinho refused to confirm details of the incident, which apparently happened after England beat Scotland last Friday, or comment on media reports that Rooney had been drunk at the team hotel the following day, but said the striker had been training successfully since returning to United this week.
"Over the last two or three days (Rooney) trained like everybody else, he wants to play like everybody else, he’s ready. What happened in the national team happened in the national team, I don’t comment," he said on Friday.
"Sometimes (players) come back stronger than when they left us because something good happened there, positive for them, other times injuries, sometimes big injuries, sometimes frustrations because they didn’t play or the result was bad.
"In this case, we knew what didn’t go well but the national team is a different chapter and is closed now until March."
The behaviour of the England captain has prompted a wider FA investigation into player behaviour on international duty after pictures, which Rooney admitted were "inappropriate", emerged of him at a wedding in the England hotel the day after the Scotland game. British media claimed the images showed him drunk.
In a combative performance, Mourinho also looked ahead to Saturday's encounter with Arsenal and his old rival Arsene Wenger by accusing the British media of not giving him the respect he is due for winning three league titles in England.
"Tomorrow is a match between the two managers with the best record in the Premier League...I think six or seven Premier League titles, I’m not sure. I have three I think and Mr Wenger has three.
"Does that mean we should be respected even in periods where our results are not the best? I think Mr Wenger has that respect from all of you, I don’t think I have. My last Premier League title was 18 months ago not 18 years ago, I don’t get that respect, to be honest."
Mourinho is under pressure following a disappointing start to the season which leaves United sixth in the table, six points behind fourth-placed Arsenal and eight points off leaders Liverpool.
Although the Portuguese has never lost a competitive game in 13 meetings with Wenger, United will be weakened on Saturday by the suspension OF Zlatan Ibrahimovic and injuries to Eric Bailly, Chris Smalling and Antonio Valencia.
He will also face an Arsenal side unbeaten in 16 games, who boast the best away record in the Premier League this year: they have not lost since going down 3-2 at United last February, a game in which Marcus Rashford scored twice on his first league start for United.
In Ibrahimovic's absence on Saturday, Rashford is expected to start in the central striker's role, but Mourinho gave few clues as to the likely lineup other than to confirm that Luke Shaw was now fit after a leg injury.
(Reporting by Neil Robinson; Editing by Toby Davis)
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