Rooney drunkenly gatecrashed a wedding at England's hotel in Watford on Saturday.
Rooney started England's 3-0 World Cup qualifying win over arch-rivals Scotland at Wembley on Friday, a match in which he suffered a knee injury that ruled him out of Tuesday's 2-2 friendly draw at home to Spain.
But in between those matches British tabloid The Sun alleged Rooney drunkenly gatecrashed a wedding at England's hotel in Watford, north of London, on Saturday.
The newspaper said the 31-year-old Manchester United star had been drinking and published a photograph of him looking the worse for wear.
A statement issued on Rooney's behalf to Britain's Press Association said Wednesday: "Naturally Wayne is sorry that pictures taken with fans have been published today.
"Although it was a day off for the whole squad and staff, he fully recognises that the images are inappropriate for someone in his position.
"Earlier today (Wednesday) Wayne spoke privately to both Gareth Southgate and Dan Ashworth to unreservedly apologise.
"He would like to further extend that apology to any young fans who have seen these pictures."
Earlier, an FA spokesperson said: "All England personnel have a responsibility to behave appropriately at all times. We will be reviewing our policy around free time whilst on international duty."
Following the Spain match, Southgate was adamant that Rooney had not been left out as a disciplinary measure.
"Wayne picked up an injury in the game (against Scotland) on Friday," said Southgate. "He couldn't train on Sunday and that's it."