Carrick did not train at Carrington on Monday morning and was also absent when United left Manchester at lunchtime.
But rather than being rested, Ferguson confirmed the England man was not well enough to be considered.
"Michael did not report. He is in bed with a virus," said Ferguson.
The United boss also confirmed veteran wide-man Ryan Giggs left training after also feeling unwell, while Paul Scholes was not considered due to the exertion of completing the full 90 minutes in Saturday's 3-2 home defeat by Tottenham.
"Ryan had a bit of a virus," said Ferguson. "He was feeling a bit rough so we sent him home. Paul Scholes played ever so well on Saturday but he is 37 now and we couldn't expect him to play three days later at his age."
United received some welcome good news on Monday morning though when Jonny Evans was able to train.
Evans needed to be helped off at the end of United's 3-2 Premier League defeat to Tottenham. And whilst Ferguson claimed the Northern Ireland international was only suffering from a dead leg, with so many defenders already injured, there was a worry Evans was about to join the casualty list.
It does appear he will be available, though, and Rio Ferdinand was also present.
Ferguson has changed his side's European routine this season, meaning they will do all their preparatory work at home before flying to Romania on Monday afternoon. Scott Wootton and Michael Keane were also amongst those training with the first team, suggesting at least one of the youngsters will make the trip.
United take on the Romanian champions knowing if they can return to England with maximum points, they will have one foot into the knockout stages as both sides won their opening games. And that at least would be one objective for the season completed after last season's unexpected exit at the group phase.
"The Champions League is completely different to the Premier League," said Wayne Rooney. "If you are not at your best you get punished, which is what happened to us last season.
"We have to make sure that won't happen again this year so this is a big game for us. Hopefully we will get a win which will put us in a good position to go through so early on in the group."
After transforming United's performance, if not the result, at Old Trafford on Saturday, Rooney's contribution against Tottenham must surely put him in line for a start.
The 26-year-old is certainly up for the challenge given how highly he still rates the Champions League experience.
"It still think it is exciting," said Rooney. "It is a great competition to be in. You look at the teams involved and it is a great challenge for everyone. It is something I love playing in."