From February 1, she will become director of customer delivery at the carrier.
Carter took over the retail remit a year ago, after the departure of Kathryn Darbandi.
Tui said a new director would be announced “in due course”.
The company said: “Jill – who has been with the company for 25 years – will use her extensive retail background, proven leadership and collaboration skills as well as passion, commitment and a strong focus on results, as she takes on this exciting new challenge.”