The Irish centre half has been out of contention since September with a cartilage problem, but was looking to return in time for the Christmas period.
Maher damaged the cruciate ligament at the time he picked up his cartilage problem against Darlington, but the club were confident a period of rest would alleviate the problem.
However, he suffered a setback in training last week and has been told he will have to go under the surgeon`s knife which will rule him out for the remainder of the season.
The Cherries have admitted he could have had the operation two months ago, but feel his effort to avoid surgery could work in his favour in the long run.
Physio Jim Marshall, speaking to the club`s website, said: "When Shaun originally damaged his knee, he also damaged his anterior cruciate ligament.
"He was given two options. He could go down the rehab path, strengthen the leg and see how it responded to football type movements. The next option was to go for a straightforward operation to reconstruct the ligament.
"I think sensibly and rightly he chose the rehab path and I think in the long run it will work in his favour.
"He was progressing really well and we were hopeful that he wouldn't have needed the operation, but last week during a low intensity drill under my supervision, he felt his knee just give way slightly.
"It doesn't appear that this has caused damage to the knee but what it does mean, is that it won't be stable enough to undertake the pressures of football training.
"Rather than cause any further damage we thought it would be best to get the operation done now."
