Councillors today voted to end free fares for 5- to 12-year-olds in Dunedin and Queenstown.
Children will have to pay $1.50 to ride the bus from late September.
Adult fares will rise from $2 to $2.50 (with a Bee card).
The Otago Regional Council said in a statement the change was "a difficult decision to make, knowing the impact it will have for people".
Community feedback on the Regional Public Transport Plan showed 89% of submitters wanted free child fares retained.
Public and active transport committee co-chair Andrew Noone said the government required councils to increase the amount of public transport funding from fares.
"We will be outlining our disappointment that the policy we have to work within is not flexible enough or fit for purpose to consider local conditions, especially regarding child fares,” Cr Noone said.
