Updated January 21, 2019 12:08:00

Photo: Shane Flanagan says his decision to resign is in "the best interests of the entire club". (AAP: Julian Smith)

Shane Flanagan has resigned from his position as head coach of the Cronulla Sharks only weeks after the NRL deregistered him for integrity breaches.

Flanagan was found to be heavily involved in club matters, including player recruitment and retention, in 2014 during his one-year ban for involvement in the club's peptide scandal.

While Flanagan says he intends to respond to the NRL's notice of deregistration at a later date, he has made the decision to stand down, "in the best interest of the entire club".

"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.

"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."

Club chairman Dino Mezzatesta thanked Flanagan for his work during a lengthy spell as Sharks coach, and in particular for delivering Cronulla its first NRL premiership in 2016.

"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," Mezzatesta 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."

'If you haven't got integrity, you haven't got anything'

Flanagan's position was put in jeopardy by the December ruling handed down after an integrity unit investigation into his conduct during the 2014 suspension.

Photo: The Sharks' 2018 season was ended by Melbourne in the preliminary final. (AAP: Steve Christo)

Along with his deregistration, the Sharks were fined $800,000, including the suspended $400,000 from the fine imposed after the supplements scandal in 2013, for which Flanagan was originally suspended.

In handing down the decision, NRL chief executive Todd Greenberg said the unit had found "a substantial volume of material" that proved Flanagan's involvement with the club at the time.

"Part of those conditions [for Flanagan's ban] was a requirement that the club not allow Mr Flanagan to be concerned directly or indirectly with the club whilst he was suspended," Greenberg said.

"That message was reinforced a number of times to Shane Flanagan and the Cronulla Sharks. They were crystal clear."

Sharks chief executive Barry Russell expressed his disappointment at the time, but accepted the NRL's decision.

"As CEO of the club, we have to accept responsibility that we broke the rules and if you break the rules, there are consequences," Russell said.

"We are paying for those right now. If you haven't got your integrity, you haven't got anything."

Cronulla says it will make a decision on its new coach for the 2019 season in the coming weeks.

Topics: nrl, rugby-league, sport, cronulla-2230, nsw, australia

First posted January 21, 2019 11:35:52