Waters had pins and plates inserted into the shoulder in August, but an injury suffered before Christmas meant they had to be removed.
News Ltd reported on Sunday that the 27-year-old would be excused from contact training throughout January and would likely miss the NAB Challenge.
The Eagles' first Challenge clash is against Fremantle at Joondalup on February 18.
Waters managed just seven games last season after gaining All Australian honours in 2012.
