Morris and fellow assistant Jim Dymock were appointed caretakers when Flanagan was sensationally de-registered by the NRL for dealing with the club while suspended in 2014.
It remains unclear whether Flanagan will appeal the ban, however the Sharks opted to give Morris the nod before the pre-season recommences on Monday.
Sharks chief executive Barry Russell and the club board began discussions on handing the reins to Morris prior to Christmas, before informing senior players on Thursday.
