The Spaniard tore the anterior cruciate ligament in his left knee, attempting an acrobatic volley in Bayern's 2-0 defeat to Borussia Dortmund in the DFL Supercup.
Martinez will require surgery and faces several months out, forcing Bayern into a rethink ahead of the new Bundesliga season.
"We can all see that we now have to do something," technical director Michael Reschke told Sport1.
"We're going to make some considerations.
"There has only been one sad moment since I joined Bayern [in June] and that was Javi's injury.
"We knew right away in the stands that something bad had happened. It's more than just sympathy for him, we're all completely numbed.
"Javier is a great lad and it's really sad what has happened."
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