Newman, 19, stormed from Claremont Oval on Saturday at quarter-time after collecting one possession for Swan Districts in a WAFL game, grabbed his bag and left the ground.
The Eagles and the Swans were both initially unsure what had occurred.
Newman met with the Eagles on Monday and it was decided he would take compassionate leave.
He is facing grievous bodily harm charges from an incident at a nightclub in Perth's Northbridge last November.
The Eagles released a statement on Monday night emphasising their support of the troubled forward.
"The club is supporting Murray through this period and we ask that people respect his privacy as he deals with this matter," the statement said.
"The club will make no further comment on the issue."
After the alleged nightclub incident, Newman returned to pre-season training in poor physical condition, finishing behind coach John Worsfold in a 2km time-trial.
Newman, who played four matches for West Coast in his debut season in 2012, is out of contract at the end of the 2013 season.
