Barrett passed concussion tests after leaving the field in the first half of the All Blacks 25-24 victory over the Springboks in Cape Town last week but reported to feeling unwell, did not return and has since suffered headaches and minor dizziness.
Pressed on whether the head injury assessment testing was effective, Hansen battered away potential concerns.
"It's one of those things. Head knocks are pretty complicated. We've had guys that have failed it because they can't remember the numbers and they're as good as gold the next day. The system is there to protect the player and in this case he passed it but the doc said he wasn't feeling great so we protected him.
"I've got a lot of confidence in the system, and in our doctor. We've got a lot of understanding of what we will and won't do with our players when they are injured and we're clear about it.
"Early in the week we discovered Beauden wasn't quite right so we're not prepared to risk him. He trained well today in the earlier session with some weights and the doc is pretty happy with where he is at."
Hansen also explained his rationale for selecting openside Matt Todd over Ardie Savea on the bench.
"Ardie has had a massive year. He didn't miss too many games for the Hurricanes and at the same time we've been trying to put size on him which he's done really well. We just think giving him a bit of a breather at this point will be good for him.
"Matt is playing particularly well, especially on the physical defensive side of the game and over the ruck. That's probably what's got him the nod ahead of Ardie. We've always said there's not a lot between them."