Guardiola took over a team that won a treble last season the Champions League, the Bundesliga title and the German Cup under predecessor Jupp Heynckes.
"Otherwise, we are going to get problems. I am a great friend of my players when they accept what I say. I support those who accept my decisions those who do not understand this will find themselves sitting in stands often," Guardiola said.
Bayern's list of long-term injuries include Spain midfielders Thiago Alcantara and Javi Martinez, and defender Holger Badstuber, as well as midfielder Xherdan Shaqiri, who picked up a hamstring problem last week playing for Switzerland.
Guardiola said he has to rotate players because of the many games in the season and that every player is needed.
"Looking at the entire season, it's not good when for example Franck Ribery or Philipp Lahm play 90 minutes every three days. The more players I have the more I can vary things," the Spaniard said.
The former Barcelona coach said he and his family have settled down well in Munich.
"I hope that I can work for a long time in Bayern, to get to know the city and the region better," Guardiola said.
Guardiola's contract runs through mid-2016.