Aguero has missed two games since limping out of last month's victory over Southampton with a heel injury and will again be absent as they host Borussia Monchengladbach in the Champions League on Tuesday.
Both manager and player have played down the problem but the 27-year-old also seems unlikely to return before the Barclays Premier League visit of Swansea on Saturday.
Asked if the injury was proving more serious than thought, Pellegrini said: "No, but it is an injury that he cannot work (on)
He needs time to recover from that problem but it is not a serious injury, it is a pain injury.
"We hope (he will return this week) but we must see the way he improves in the next days
When he can run with normality he can work but if he cannot operate with his heel it is very difficult for him to do."
Pellegrini is also uncertain when influential captain Vincent Kompany might be back in the reckoning.
The Chilean said: "Vincent is improving
He is doing some tests on his calf, on which is the best way for him to improve
We will see in the next days when he can return."
City have had problems with injuries throughout the campaign
Kompany has missed the last five games with a calf problem while Aguero also had an earlier spell out with a hamstring issue and David Silva only recently returned after a near two-month absence.
Samir Nasri is a long-term casualty, Fabian Delph missed most of the opening three months of the season and other key players such as Joe Hart, Yaya Toure and Pablo Zabaleta have had time out.
All of this could be a factor in City's recent patchy form, which continued with a 2-0 loss at Stoke on Saturday, but Pellegrini claims it is too early to assess the performance of back-up players.
Speaking at a press conference, he said: "I always say I prefer to play with the whole squad then I can choose the best XI starters, but if the starting XI has six or seven players injured we must make a balance of the whole season
You cannot have a conclusion after one game."
Asked directly if the likes of Wilfried Bony, Nicolas Otamendi, Martin Demichelis or Eliaquim Mangala were not delivering, Pellegrini said: "I analyse the individual performances with the players, not with the press."
Toure is fit to return but with another six on the sidelines, Pellegrini is unlikely to make many changes this week.
He said: "It will be the fifth game we play in 14 days, and for the last two we had less than 72 hours to recover
It is a difficult game because (we have had) too many games for the same players but we need to make an important effort to try and finish at the top of the group
We need to concentrate more than on Saturday."
City can only top Group D if they beat Monchengladbach and leaders Juventus slip up at Sevilla.
After finishing second and drawing Barcelona in the last two years that was a clear aim, but Pellegrini said: "I think Chelsea, (Manchester) United and Arsenal would like to be in our position
"If you don't finish at the top of this group, I don't think it is disappointing because we had to play twice against Juventus and we didn't beat them
"If we don't win, I think we qualify but not in the way we wanted
After that I don't think we have to be always pessimistic about the draw."
Source : PA
Source: PA