The Austrian took a tumble during training on December 5, sustaining a broken tibia, fibula, and ankle joint, Red Bull KTM Factory Racing has announced.
There has also been a scare for team-mate and 2023 Dakar Rally winner Kevin Benavides after a separate incident, but the Argentine is expected to start the prologue in AlUla on January 5.
Walkner, though, has already undergone surgery in California and will need another operation at some stage, with the aim being for that to occur at home.
“It's been a very difficult few days for the team here in the United States,” said Rally Team Manager, Andreas Hölzl.
“Training for the Dakar had been going extremely well, with all riders working very hard.
“Kevin damaged his leg last Sunday, but thankfully, it wasn't too bad. We hope he will be back to near full fitness by Dakar.
“On Monday, Matthias had a nasty crash while training, which ended up in him having several fractures.
“The surgery went really well, and they have attached a fixator to his left leg to help the recovery. But he will require more surgery, once the swelling starts to go down.
“Obviously, these two incidents have been a massive blow to the team, but we will continue to look ahead and do all we can to be as strong as possible for Dakar.
“The whole team wishes both Matthias and Kevin a quick and full recovery.”