The Morocco international could miss both legs of the Champions League quarter-final against Porto this month due to a muscle injury picked up in Wednesday's German Cup quarter-final win over Bayer Leverkusen.
"We had problems and now we have more problems. Our situation is very critical, very critical," Guardiola told reporters.
"I never had a situation with so many injuries. But we are here. We will fight until the end for our goals, our club."
Bayern, top of the Bundesliga with a 10-point lead, are chasing a treble of titles, hoping to repeat their 2013 achievement. They travel to Porto next week for the first leg of the last-eight tie.
But Benatia's injury, which could sideline him for up to a month, is a further blow with Bastian Schweinsteiger, David Alaba, Arjen Robben, Javi Martinez and reserve keeper Tom Starke already on the injury list.
Franck Ribery, who has been out for five weeks with an ankle injury, returned to training this week but Guardiola said he was doubtful for the game in Porto.
"I still do not know if he can travel on Monday with us to Porto," he said.
Thiago Alcantara has only just returned to action after a year out injured.
"I have full confidence in my team. I have learned a lot about my players in the last two games. They showed a lot of passion and when you show that then you can win a lot of things," Guardiola said.
(Reporting by Karolos Grohmann; Editing by Editing by Ed Osmond)
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