Charlton will play Championship football next season after manager Bowyer led the club to League One play-off final glory at Wembley.
Although the former Premier League midfielder’s contract is due to expire at the end of the current month, fans assumed that his stay would be extended after he secured an unlikely promotion.
However, the club have now revealed Bowyer has refused their offer of a one-year contract even though it is worth six times as much as the deal he took when he became caretaker boss in 2017.
The statement read: “Charlton Athletic have been unable to reach an agreement with manager Lee Bowyer regarding the extension of his contract.
“The fact the club is for sale has not helped with finding an agreement. The current owner needs to take into account that a new owner may want to appoint his own manager.
“However, this concern did not stop the current owner proposing a contract extension of one year to Lee Bowyer, even though the club may be sold in a few weeks.
“Under those circumstances a multi-year extension would not be good business practice.
“In addition, since the club is still losing money, which is one of the reasons why the club has not been sold yet, the focus on reducing costs means that we are extremely limited on payroll increases.
“Lee has been offered a one-year extension to his contract at a level which is approximately three times what he had since his last increase when he became permanent manager in September.
“It is six times what he earned when he started as assistant manager in 2017 and 50% more than what any Charlton manager previously had (excluding the Premier League years).
“This reflects the strong desire we have to continue to have Lee as our manager. But Lee wanted much more.”
The failure to reach an agreement has left the club in disarray ahead of their first Championship campaign in four seasons.
The club went on to slam the way in which current Championship club owners decided to accept losses, and outlined that their current takeover talks makes planning for the future difficult.
The statement continued: “The owner understands Lee’s point of view, because many Championship clubs pay huge amounts to their manager.
“It is fair that Lee feels he should be paid like many other Championship managers. That the average Championship club makes a loss of around £15 million per year is not something players should care about. The owners are crazy.
“This is why we could not come to an agreement. Another element may have influenced as well. Unlike previous contract discussions, Lee wanted an agent to handle it.
“We reluctantly accepted. However, involving a player agent in a manager’s contract discussion is not healthy. If the agent helps make the manager more money, it may result in the manager to have a more positive attitude towards players proposed by the same agent, a conflict of interest.
“Obviously, Lee is above such things, but it is nevertheless not a healthy situation.
“The club hasn’t started to look for any other manager in the meantime and does not intend to appoint a permanent manager, since the club is going to be sold.
“A caretaker manager will be announced in due course and in the meantime the other staff members will continue to prepare the upcoming season for which a lot of good work has been performed already.
“If Lee does change his mind before his contract expires and chooses to continue his good work at Charlton, he is still welcome to stay.
“However our ability to sell the club is the most important thing right now.”