Flanagan sat in a corporate box in the Andrew Ettingshausen Stand as the Sharks lost 28-22 to Wests Tigers.
The move appears to be in violation of his 12-month ban handed down last December in regard to governance issues at the club in 2011.
Flanagan is appealing the ban, which is currently being reviewed by the game's governing body.
The NRL have launched an investigation into the incident and if Flanagan is found guilty of breaching the ban, he could face a fine or an extension of his suspension.
"We have asked the Sharks to give us an explanation and we are waiting for that explanation," NRL boss Dave Smith said on Monday after presenting the NRL annual report.
"We have been very clear about Shane's position as we go through this process.
"We have asked for information and until we receive that it is impossible to say if it is a violation or not.
(But) I think the rules are clear ... `direct and indirect involvement'.
"Once we get the facts back we will make a determination.
"There are a number of things within the rules that we potentially can do if there has been a breach.
"We have made a request and I know (Sharks chairman) Damian Keogh and (chief executive) Steve Noyce are working on that and once we get that we will be able to be really clear about that."
Former Canberra winger Sandor Earl is the only player issued with an infraction notice in either code more than 12 months down the track into ASADA's investigation.
NRL chief operating officer Jim Doyle said Earl was continuing to co-operate with the Australian Sports Anti-Doping Authority on the issue.
"At the moment obviously Sandor and his legal team are still working with ASADA as to the level of substantial assistance," Doyle said.
"Once they have concluded their discussion we will be looking to take this forward."
Smith said the ASADA issued has become clearer since the so-called `darkest day in Australian sport', February 7 last year, but could not give a timeline for a conclusion of the protracted investigation.
"As part of this process, as difficult as it was, the allegations were incredibly serious and complicated, I felt it would take a while for the investigators to investigate and for the facts to become clear," Smith said.
"Frankly that's why I have managed it they way I have managed it. It wasn't clear, it has become clearer as we have managed to establish the facts
"But I can't put a specific date on it."