Newry City chairman Paul McKenna has denied interfering in team selection while Gerry Flynn was manager.
Flynn resigned on Tuesday night because of "things going on behind the scenes", and McKenna has admitted the pair had disagreements in the past.
McKenna said he merely discussed first-team matters with Flynn.
"No individual at Newry, including myself, has interfered with first-team selection or demanded particular player inclusion or exclusion," he explained.
He added: "It is my prerogative as chairman and as one of the club's senior custodians to discuss first-team matters with the manager, as I do with the reserve team management, and the Academy staff to ensure that the football department is moving in tandem with off field activities.
"Like many football clubs and football club officials, we have experienced difference of opinions and have had disagreements, however I never felt at any stage relationships had broken down to such a degree as to warrant resignation.
"I wish to make it clear to all involved with the club that I will work in close proximity with all relevant Club personnel to rectify this situation as quickly, seamlessly and painless a fashion as is possible, and as swiftly as possible to ensure minimum disruption to the football department at the club."
However, Flynn says he was left with no option but to resign as manager.
"It had got to the stage where I wasn't enjoying the role I was in and it was not a knee-jerk reaction," said Flynn.
"There were some things going on behind the scenes which made it impossible for me to continue and I could never see myself managing another club.
"I've been overwhelmed by the messages of support and am just trying to get my head around what has happened."
Flynn announced his departure as Newry boss after Tuesday night's 2-1 win over Coleraine and added that he left with "a heavy heart".
"I'm trying to come to terms with what has happened and I am grateful for the messages of support by email, text and phone," he said.
"I thought long and hard about it and it is with a heavy heart that I left and I'm now wondering what I'm going to do with myself on Saturday afternoon.
"I'm totally gutted, but grateful for having had the chance to manage Newry City, and I wish them all the best for the future."
It is understood that players at the club are unhappy with the situation which culminated in Flynn's departure.
They are believed to have sought a face-to-face meeting with the board.
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