The Sharks have been fined $800,000 - half of which was suspended at the time over their supplements saga.
Flanagan and the club have until the end of January to respond to a breach notice, which is when the NRL will make its final determination.
However, the Sharks will have to overturn evidence found by the NRL integrity unit that more than 50 emails were sent by Flanagan concerning retention and recruitment.
His first correspondence was sent just weeks after his suspension and continued all the way to September 2014.
