Most fares on buses, trains and a harbour ferry in Wellington increased by 50 cents - $1 on Monday.
Wellington Regional Council says the rise, which is the first in two years, is necessary to meet a $5 million shortfall from rising labour and fuel costs.
The move has upset some commuters, particularly on the Paraparaumu rail line, who have complained about crowded trains and a lack of carriages.
But the council says it plans to introduce 10 new carriages before Christmas, and new trains are scheduled to arrive in 2010.
It doubts that the rises will have a long-term effect on patronage.
In Auckland, increased fares to Waiheke Island are being protested by transporting a coffin containing at least 600 signatures across the Hauraki Gulf on Monday morning.
Island residents say fares on the Fullers ferry have risen by 52% in six years.
They want the Auckland Regional Transport Authority to consider subsidising the route.
