Putin acknowledged, not for the first time, that the call-up of 300,000 reservists that he ordered in September had not gone smoothly.
"The partial mobilisation that was carried out revealed certain problems, as everyone well knows, which should be promptly addressed," he said.
Putin also referred to other unspecified problems in the military and said that constructive criticism should be heeded.
It was the latest in a series of recent comments in which Putin has acknowledged, albeit obliquely, the challenges his army is facing.
Shoigu proposed raising the age for mandatory Russian military service to a new range of 21-30, compared to 18-27 at the moment.