Paul Scholes resigned from his position as Oldham manager by text, according to owner Abdallah Lemsagam.
The 44-year-old lasted 31 days at the League Two club but said he could not "operate as I intended and was led to believe prior to taking on the role".
But Lemsagam said he was "surprised by the reasons" that the former Manchester United midfielder has given.
The Moroccan added he had given Scholes "all the support and autonomy that he asked for".
He continued: "I have been in Dubai over the last couple of weeks and was at ease knowing that he was in charge.
"I was very surprised as he simply resigned by text on Wednesday afternoon and has refused to discuss matters that influenced him to make his decision.
"Paul and I both agreed that there is potential but I reassured him that he had my full backing to rebuild the team of his choice next season.
"He did not raise any concerns at all about the team or any other matters informally or formally, prior to his resignation. He gave no opportunity or indications that he needed to address any issues at all."
The Latics have placed coach Pete Wild in caretaker charge for the second time this season.
Wild led the team between Frankie Bunn's sacking in December and Scholes' appointment, guiding them to an FA Cup win over Premier League Fulham.
Scholes 'reassured he was in charge'
Scholes' first foray into management began on 11 February and he was only in charge for seven games, winning one of them.
The former Manchester United and England midfielder took over with the Latics 14th in the table, nine points off the play-offs, and leaves with them in the same position.
Scholes said he took the decision with "great regret".
Lemsagam has started work on finding Scholes' replacement.
He added: "I personally was always supportive of any decisions Paul made or consulted me on, reassuring him that he was the man in charge.
"I continued to encourage him despite the results and reassured him that his job was secure. I was content to remain in League Two for this season and working with the team we have for the remainder of this season is important.
"Management is a difficult job and both myself and everyone at the club would have worked with Paul to find solutions, had we been given the chance."
Oldham continue their League Two season on Saturday at home to fifth-placed Tranmere Rovers.