The England striker played in the 1-0 Premier League win at Swansea on Saturday and there were no signs that he was injured, but he was not present when training got underway.
There was no immediate word from United about whether Rooney was injured, with Sir Alex Ferguson likely to offer an update during this his pre-match press conference later on Monday.
Also absent was Northern Ireland defender Jonny Evans.
Defender Chris Smalling and striker Danny Welbeck, who both missed the weekend trip to south Wales because of injury, trained in a small group away from the main session, although previously Ferguson had indicated Smalling might be fit for Tuesday’s game.
Meanwhile, Inter Milan’s flight to Turkey on Sunday was held up after Argentine forward Mauro Zarate forgot his passport and had to return to the club’s training ground to get it.
It wasn’t the first time Inter have faced unexpected obstacles when coming up against the Turkish club.
When the two sides met in their opening Group B match at the San Siro in September, minnows Trabzonspor stunned their illustrious hosts by snatching a shock 1-0 victory.
It was the beginning of the end for then Inter coach Gian Piero Gasperini, who lasted only two more matches before being fired.
But as the two sides prepare to meet here on Tuesday, Inter are safe in the knowledge that a point will be enough to see them into the knock-out stages with a game to spare while a victory would assure top spot in the group.
It has been a remarkable turnaround for Inter having lost what on paper appeared to be their easiest game in the group, at home to the rank outsiders.
But now they are focussed on claiming first place and hence probably avoiding potentially tough second round clashes against the likes of Barcelona, Manchester United, Real Madrid and Bayern Munich.
What’s more, having had a disastrous start to their scudetto campaign, they are still down in 16th after 10 games, and centre-back Andrea Ranocchia says they really need to get qualification for the second round out of the way so they can concentrate on climbing up the Serie A table.
“We want three points for the last 16 which is an important step we need to take,” he said.
“We need to put this question to bed so we can think about the league.”
Inter arrive in Turkey without playmaker Wesley Sneijder who has a thigh strain and will be out for around three weeks.
He pulled up with the problem during the warm-up for Saturday’s 2-1 win over Cagliari but his replacement Coutinho scored the winner.
Coutinho arrived last season with a big reputation as the next big thing to come out of Brazil but having been thrust straight into the first team due to injuries, he struggled for form and lost his way, also getting injured himself.
But after his positive impact against the Sardinians, he may be given the creative trequartista role again behind the front two.
Inter are also boosted by the return of defenders Lucio and Yuto Nagatomo after missing out at the weekend.
Trabzonspor didn’t start their league campaign well but are now back amongst the front-runners and challenging Fenerbahce for the championship, as they did last season.
They are four points behind Inter in the group and level with CSKA Moscow but must claim more points than the Russians in their final two games if they are to progress as they have an inferior head-to-head record, although Lille are not yet out of it either.