Queensland State of Origin representative Hunt signed a contract extension with the Dragons in October last year that tied him to the joint venture until the end of 2025.
But when the club sacked close ally Anthony Griffin as coach last month, speculation mounted that Hunt could lobby to follow him out the door, having previously pushed for a contract clause that would have tied his future to Griffin's.
Widely regarded as one of the best halfbacks in the game, Hunt had been linked with Canterbury and Gold Coast, while Canberra and Wests Tigers also have the wherewithal to make a play for him for 2024.
But Flanagan confirmed on Saturday that Hunt was part of his plans and that a release would not be entertained.
The Dragons told Hunt he would not be allowed to leave but the playmaker is expected to meet with Flanagan and club powerbrokers following Wednesday's second Origin game.
"Ben is contracted through to the end of the 2025 season and is a big part of the current and future plans of the Dragons as the club builds towards achieving sustained success in the coming years," Dragons chief executive Ryan Webb said in a statement.
"We're committed to working with Ben to understand and address his concerns as we all have the same goal of building a strong and successful club."
Dragons centre Zac Lomax admitted the release request had caught him off guard and said he was hopeful Hunt would change his posture.
"We probably didn't see it coming," he told Fox Sport's Sunday Night With Matty Johns.
"Benny is his own man and he's going to make his own decisions but us as players, we'd obviously prefer 'Dozer' to be with us. He obviously makes our team such a better team.
"It's going to be his decision and I'm sure he'll make the right one."
Prop Blake Lawrie said he had not contacted Hunt to discuss the situation.
"He's got a pretty big game to prepare for on Wednesday night," he said.
"Obviously Benny Hunt and 'Flanno' will talk going forward and whatever happens will happen.Â
"He's our captain, he's our leader. A bit selfishly, I don't want him to go anywhere."
Webb will front the media in Wollongong on Monday morning to address the situation.
Concerns about Hunt's commitment to the Dragons had already been raised this week when he told reporters during Queensland's State of Origin camp that he didn't know how Flanagan's appointment would affect his future.
Flanagan called Hunt before he had been confirmed as head coach to express his desire to field the 33-year-old at halfback rather than hooker, where he reluctantly spent time earlier this season.
Entrenched in the bottom four on the NRL ladder, the Dragons are at risk of missing a fifth consecutive season of finals but Hunt has been their shining light throughout the string of poor results.
He is the side's only current Origin representative, finished third in the Dally M rankings last season and looms as critical to their rebuild under Flanagan.
