Murphy hurt his leg sliding into second base on Saturday.
Baker would not pinpoint exactly what is bothering the team's big free-agent acquisition from this offseason.
"I'm sure the world would like to know [what's wrong with Murphy]," Baker told reporters on Wednesday. "Our trainers are still working on him. They are trying to get to the bottom of it. When you are hurt this late in the season, you don't have a bunch of time to come back. We have some hands working on him."
The Nationals entered Wednesday night leading the NL East by eight games. Offensively speaking, Murphy has been a big reason why. He's hitting .347, with 25 home runs and 104 RBIs.
"Daniel has been carrying us most of the season, so now it's time for some of the other guys to step up during Daniel's absence and not depend on Daniel being here," Baker said.