The one-time All Black has only just returned to the field after a year out with concussion symptoms, making his return 11 days ago in the Chiefs' 46-17 win over the Reds in New Plymouth.
But the headaches that plagued the 26-year-old throughout 2016 returned after training, with no apparent cause.
RNZI reports Ngatai will sit out the Chiefs' match against the Crusaders in Fiji, with Anton Lienert-Brown moving over to second-five and Sam McNicol slotting into centre.
"Charlie developed a headache after training and we're not sure why, but we're taking a precautionary approach," Chiefs assistant coach Andrew Strawbridge said.
"We want to look after him."
The Chiefs have made four other changes to their starting line-up for the clash in tropical conditions.
All Blacks hooker Nathan Harris will make his first start of the season after recovering from an ACL tear, pushing veteran Hika Elliot to the bench.
First-five Aaron Cruden has recovered from a head knock and will co-captain the side, while Tim Nanai-Williams will make his long-awaited return on the right wing.
Nanai-Williams has been out for more than two months after dislocating his shoulder, and replaces the dropped Toni Pulu.
Stephen Donald has been named in the reserves.