And the Sharks have also sacked football manager Darren Mooney and head trainer Mark Noakes.
Top sports news outlet The Daily Telegraph made the stunning revelation late Friday afternoon, ahead of the Sharks' NRL season opener against Gold Coast Titans on Sunday night.
Flanagan's dismissal falls hot on the heels of continuing claims that up to 14 Sharks players could be stood down as a result of ASADA's investigation into possible use of performance enhancing drugs in recent seasons.
It is unclear just why Flanagan was dismissed at such short notice.
Flanagan's dismissal came after he met with ASADA investigators on Friday to answer questions about the unfolding drugs scandal.
Flanagan has been Sharks coach since 2010.
The height of ASADA's full-scale investigation is believed to centre around alleged banned substances use in the 2011 season.
Cronulla still does not have a chief executive.
Peter Sharp will hastily take over the reins of the Sharks ahead of the season opening match in just two days' time.
The NRL reassured fans on Thursday afternoon that the game would go ahead despite concerns over Cronulla's ability to field a team.
Sharks players were reported on Friday to be considering confessing to ASADA their alleged use of substances in return for minimum playing bans.
The report claimed the players would continue to receive their full pay while serving six-month suspensions, which is the minimum under ASADA regulations if athletes come forward with information and confessions of use.