Hurricanes coach Chris Boyd confirmed Barrett missed the Hurricanes' 34-20 win over the Bulls in Pretoria, because of headaches.
It means one of the All Blacks' key men for next month's Lions series will need to pass concussion protocols to be cleared to face the Force on Saturday night.
Flanker Ardie Savea is another, along with lock Mark Abbott, after both suffered concussion symptoms on Sunday and would appear unlikely to play against the Force.
There was a glimmer of good news amid the fog, with Boyd saying All Blacks wing Nehe Milner-Skudder was a good chance of boarding a plane on Monday to return to action in Perth after a long stint on the sidelines with fractured bones in his foot.
Barrett took a head knock during the team's 61-7 win over the Cheetahs in Wellington. He passed a halftime concussion test, but was replaced 10 minutes into the second spell.
Barrett has been training well with the Hurricanes since they moved on to South Africa, but waking with headaches. Team doctors were unable to isolate or link the headaches to the blow Barrett took against the Cheetahs, but he was withdrawn from the Bulls match as a precaution.
"When we came over here he's had some headaches and the doctor was unable to differentiate between the altitude, the humidity, the air conditioning; because when you come over here on a short turnaround, the headaches and those types of symptoms are pretty normal," Boyd said.
"But the fact that he couldn't isolate those out from the back-end of the game against the Cheetahs meant that we were very cautious and withdrew him out of the game."
Barrett ran water bottles at Loftus Versfeld for the team instead, after Otere Black was named to play in his place.
Hurricanes captain Dane Coles has been out of action since March 18, partly due to the effects of a head knock. In Coles' case, the blow wasn't obvious at the time and it was only when the hooker began suffering exercise-induced headaches that the dots were connected.
"So [Beauden] was really different because every time he exercised, every time he trained he got absolutely no symptoms at all. But the next morning he woke up with a headache, which probably 80 per cent of the squad did because we're trying to get used to the altitude and trying to get used to the temperature and trying to get used to all sorts of things," said Boyd.
"But when you speak to the medical team, it's like what is inducing that? Is it a continuation of some head knock symptoms or what's going on? So we weren't able to differentiate from that and we pulled him out at Captain's Run yesterday."
It's not a newsflash to say Barrett is a good player whose health is important to lots of people. But with the heightened awareness around concussion and the British and Irish Lions' tour on the horizon, news of headaches is concerning.
In this instance, early indications are that Barrett isn't facing a serious issue and the Hurricanes have simply erred on the side of caution. There's no hard and fast rules with these things, though, and what appears to be an innocuous blow might have significant longterm impacts and vice versa.
With Ardie Savea, he looked to be out cold when he hit the deck in Pretoria, after suffering a head clash as he and wing Wes Goosen went to tackle Bulls first five-eighth Tian Schoeman.
"Ardie and Mark Abbott left the field with concussions and we won't know about them for the next couple of days," Boyd said.
They've yet to be ruled out of the Force game just yet, though.
"Everybody will go to Perth and then we'll have a look at Wes [Goosen, who suffered a shoulder or rib injury] and Ardie and Abbo, particularly, and see where they're at and if we need to make some change we will."
The Hurricanes took one fewer than their official allotment of 27 players on this trip. The plan was for either Matt Proctor (concussion) or Milner-Skudder to meet them in Perth if fit enough and it appears that decision has been made.
"At this stage, if Nehe passes a fitness test on Monday morning, he'll fly out from Wellington to join us on Monday night in Perth and be available to play against the Force," said Boyd.
Photo: Getty Images (Beauden Barrett's condition will be of big concern to the All Blacks with the Lions just around the corner).