The club's owners met on Tuesday to discuss, amongst other things, who will be in charge on Rovers' return to the Championship next season.
Flynn took over on a caretaker basis at the beginning of January following Dean Saunders' departure to Wolves and was later handed a deal until the end of the season.
The former Wales Under-21 boss led Doncaster to the league title at the weekend with a dramatic 1-0 win at Brentford.
His contract was subsequently extended by a further two weeks but it remains to be seen whether the 57-year-old will be the man in charge when the south Yorkshire outfit resume in August.
A club statement said: "After three days of celebrating Rovers' incredible League One Championship win, the owners met yesterday (Tuesday) 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.
"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."