Shane Flanagan resigned as Cronulla Sharks head coach as he faces de-registration from the NRL.

Flanagan is set to have his registration cancelled after an NRL investigation found he had dealings with the Sharks while suspended in 2014, although he intends to respond.

But the 2016 premiership coach has opted to step aside, with the Sharks having named John Morris as interim boss earlier this month.

"This was obviously one of the toughest decisions of my 36-year rugby league career to resign from the head coaching role at Cronulla," Flanagan said in a statement on Monday.

"The last month has taken an enormous mental and emotional toll on my family and myself.

"I intend on responding to the notice issued by the NRL, however I have made this decision in the best interests of the entire club and the players to allow the best possible preparation for the 2019 season without constant speculation and uncertainty as to who their head coach will be.

"I want to thank the Cronulla board and management, both past and present, as well as my dedicated coaching staff, all of whom I have worked closely with over seven seasons.

"I especially want to extend my gratitude to the many players who I have been fortunate to coach at Cronulla. Without doubt, I will hold the entire 2016 playing squad, staff, supporters and unforgettable achievement to deliver the club its first premiership, forever in my heart.

"I want to single out and thank the incredibly loyal Sharks supporters for their on-going support and last but certainly not least, I want to thank rugby league fans in general for their overwhelming support and messages over the years and more so over the past month."

Sharks chairman Dino Mezzatesta thanked Flanagan, who first took the helm of Cronulla in 2010.

"Shane was our first premiership-winning coach, he is the coach of our Team of the Half Century and he has given exceptional service and dedication to our club," he said.

"He worked tirelessly to build our team and our club into a competitive force and he will forever hold a special place in the club's history."