The tricky winger was hurt after landing awkwardly shortly before half-time of Saturday's thrilling 25-24 Rugby Championship victory over South Africa at Newlands.
It marks a fresh setback for Milner-Skudder, who was starting to hit top form again for the All Blacks following a series of injuries that saw him go almost two years without playing a Test for his country before he returned to the fold last month.
Milner-Skudder dislocated his left shoulder in 2016 and broke a foot early in this year's Super Rugby season.
A tweet from the All Blacks read: "UPDATE: Steve Hansen confirms @Nmilnerskudder dislocated shoulder. Will require surgery. Expected to be out for upto six months."
UPDATE: Steve Hansen confirms @Nmilnerskudder dislocated shoulder. Will require surgery. Expected to be out for upto six months.— All Blacks (@AllBlacks) October 8, 2017
Milner-Skudder will consequently miss the final Bledisloe Cup encounter against Australia this month and the All Blacks' November Internationals in Europe.