The Czech rider damaged his shoulder in a massive high-side at Indianapolis, and while he started at both his home Brno race and then Misano he was eventually forced to abandon his 2013 campaign due to the subsequent discomfort.
World Supersport rider Luca Scassa is filling in for Abraham in the Cardion AB team.
"Karel Abraham suffered a multiple injury to the shoulder joint," explained Igor Cizmar, senior consultant of the Trauma Department at the Olomouc University Hospital where Abraham is being treated.
"His ligaments of the articular capsule on the outside of the joint were damaged, while the ligaments connecting the scapula and the clavicle had torn and healed to form a weak join. This was causing instability in the joint and discomfort.
"The ligaments connecting the scapula and clavicle were no longer holding the shoulder in place, so it was necessary to graft on a tendon from the forearm; use of that tendon is standard and the patient will not notice it, even when playing sports to the full.
"Karel will be able to start exercising again in two or three weeks at the earliest. Gradually, we will build up the level of exercise so that he should be able to exercise fully after five or six weeks."
Abraham said he does not anticipate any long-term problems, and expects to rehabilitate fully over the winter.
"I'm happy to have got it over with it and after the rehab's finished I'm sure I'll be able to once again give 100 per cent in my training and riding," he added.
"It'll be a while of course before I'm able to get back on the bike, but I've got the whole winter in front of me and the aim is to be able to go into pre-season testing without anything holding me back."