The influential defender faces a month on the sidelines after suffering a groin injury in Monday's Premier League win over Newcastle.
It is another setback for the 27-year-old Belgian, whose two-month absence at a critical stage of last season proved damaging to City's title chances.
That lay-off - which followed a spell out for a similar problem the previous year - proved particularly frustrating as he had been pencilled in to return several times, only to have his comeback put back.
But none of that is a worry to Pellegrini, who does not see the problems as related.
The Chilean said: "I am not concerned about that. That season was one thing, this season is another one.
"Of course, he is very important to us, Vincent Kompany, but we can do nothing about it. We try to do the best we can."
If Kompany is out for a month as feared, he would miss this weekend's trip to Cardiff, next week's clash with Hull and the game at Stoke after the next international break.
He could come back into contention for the derby against Manchester United on September 22.
News of his condition will also be a concern to Belgium, who play an important World Cup qualifier in Scotland next month.
With Micah Richards also injured, Pellegrini is hoping Matija Nastasic will be fit to return in Kompany's place.
The Serbian was expected to miss the first month of the season with an ankle injury but returned to training this week.
If he proves his fitness Pellegrini would not need to consider deploying Javi Garcia in the back line, as he did in the closing stages against Newcastle.
The other option is 22-year-old Dedryck Boyata, who is hoping to revive his City career after loan spells at Bolton and FC Twente in the past two seasons.
Pellegrini said: "We have many options. Nastasic has worked this week, we have Javi Garcia and we have Boyata. We will see who is the best."
The situation has allowed England centre-back Joleon Lescott the chance to re-establish himself after falling down the pecking order under Roberto Mancini last season.
The 31-year-old is entering the final year of his contract and his future is uncertain.
Pellegrini was not willing to discuss Lescott's situation at his press conference to preview Sunday's game at Cardiff.
He said: "I know Joleon Lescott is in his last year here. We will see what happens with him.
"We are not talking about those things this week."
Lescott's form, however, has caught Pellegrini's eye.
He said: "Yes, I think he has worked very well. That's why he started the game against Newcastle."
While City may have some issues in their defence, there appears to be no problems in attack after Monday's impressive 4-0 demolition of Newcastle.
The issue for Pellegrini is whether his men can maintain such an intensity.
He said: "It's always difficult to maintain that level but we are sure that in a lot of games we are going to do it.
"Maybe some times we will win just 1-0 and defending, but we will try to do what we did last Monday in every game.
"Of course maybe sometimes we will do it better and sometimes worse but we will try."