The Oman international's current deal at the Reebok Stadium expires next summer.
Trotters chief Megson insists discussions were held with Al Habsi over the summer and it is only since agents began to interfere that proceedings have broken down.
"We talked to Ali in the summer when he didn't have a contract with an agent," Megson told the Manchester Evening News.
"That was the last time we spoke to him about his contract. To be honest we are quite relaxed about it.
"We've got Jussi (Jaaskelainen) on his long-term deal and he is doing well. We would like Ali to stay but no-one is going to dictate to the football club from outside on what will and won't happen.
"We are well stocked for goalkeepers. Adam Bogdan is only young but improving while at the other end in terms of experience we've got Ian Walker.
"But it is a subject that will be dealt with between the club and the player, no-one else."