The 25-year-old forward spent more than a week in hospital after he returned home to Perth on the morning of the club's June 10 match in Adelaide.
It has since been revealed Waterman is battling ulcerative colitis - an inflammatory bowel disease that is an autoimmune condition.
He is almost certain to miss the rest of the season and there's a small chance the illness could end his AFL career.
Waterman's dad - two-time West Coast premiership player Chris Waterman - has criticised what he described as the club's lack of communication after his son became ill.
Despite there being "confidentialities" around player welfare, AFLPA boss Paul Marsh confirmed he was looking into the claims.
"I will say that we've absolutely followed up having known about this and we want to understand the different sides of the story, then ... we'll work out where we go with it," Marsh told SEN.
"It's a concerning read, no doubt.
"Reading it, it does appear there are two sides to what happened here and we've got to work through that."
Beleaguered Eagles coach Adam Simpson, who is fighting to keep his job amid a historic losing run, said he tried to make contact with Jake Waterman, but was unsuccessful.
"A few text messages here and there but no response," Simpson said on Tuesday.
"He was quite ill at the time.
"I was unaware (of how serious it was) ... in the early stages and then it got quite severe and I still don't know the full extent of the situation.
"But it's not great. Our heart goes out to him."
Waterman is out of contract at the end of the season and could seek a fresh start elsewhere given West Coast are in the early stages of what looms as a long and painful rebuild.
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