The Bombers revealed on Thursday that the promising tall forward had pulled up sore from a training session during the gruelling pre-season program.
Daniher, 18, underwent minor corrective surgery to remove floating cartilage from around his knee-cap on Wednesday.
Essendon declared their prized youngster, who is the son of former Bomber Anthony Daniher and the nephew of Neale and Terry, will be on a restricted training program until after Christmas.
But, Bombers development manager Danny Corcoran said Daniher's pre-season would not be too heavily affected by the surgery.
"He's had a minor 'scope to clean up a bit of cartilage that came loose from his patella," Corcoran told AFL.com.au.
"He just cooled down after one of the sessions and felt a bit sore and he just reported it to the doctors.
"They had a look and found there was a piece of floating cartilage that they needed to take out."
The Bombers swooped on Daniher with their first pick of the 2012 national draft, at selection 10 overall.
Corcoran said the Bombers even expect the talented young big man to start running when he returns from the festive holidays break.
"We're expecting him to be running on day one when we return," Corcoran said.
"He's had a good six weeks before the break - he's really trained very, very well so far in the pre-season.
"He'll resume on January 7 when we're all back."