For example, a return flight on February 25 will cost $69 on the 10.30am flight and $99 on the 5.10pm return leg that day.
Other fares are available but at higher prices, but even so they are proving popular in terms of forward bookings.
Air New Zealand said the move to the larger twin turbo-prop Q300s will happen across its entire regional service.
The upgrade is due to be completed by August this year.
The airline said more seats on each flight would result in more low fares and that in this financial year it will offer more than two million domestic fares under $100.
While the bigger planes mean a 75 per cent increase in seats, it will also mean a cut in the number of flights.
There had been four return trips every weekday between Whanganui and Auckland, with three return trips on a Saturday and four on a Sunday.
But from February 3 that dropped to three return services between the two ports on weekdays.
From next Saturday there will be two outward flights and one return flight to Whanganui and from Sunday there will be one outward flight and two return flights to Whanganui.