The Welshman was appointed to the helm in January on a deal until the end of the season when Dean Saunders departed for Wolverhampton Wanderers.
However, despite the fact that he has guided the team to automatic promotion, it has been revealed that no verdict has been reached as to who will be in charge in the Championship.
"After three days of celebrating Rovers's incredible League One Championship win, the owners met yesterday to consider who will lead Rovers in their new challenge as they return to one of the most competitive leagues in the world. The hard work starts now as planning for the new season begins behind the scenes as the dust settles on the celebrations," read a statement on the club's official website.
"As the club are now at an important stage in planning for the new challenges ahead, the owners discussed the manager and players for the new season. These discussions are still on going as the owners work hard to give the club the best chance to compete in the Championship. The club hope to clarify the position on Friday this week."
Flynn has never previously managed a side in the second flight of English football.