Mr Lambert said the changes would reduce the "inequity" between train fares and those of other public transport.
"For a number of years train users have enjoyed significantly lower fares than bus users...
"This year's increase in rail fares removes that inequity with bus and simplifies the fare structure."
The changes were needed ahead of the introduction of the HOP transport payment card system for train services later this year, Mr Lambert said.
Students will face higher ticket prices across the board under the new structure, with a ratepayer subsidy on their fares reduced from 40 per cent to 38 per cent.
One stage bus fares will go up 10c and inner city bus tickets will double in price for adults and children to $1 and 60 cents respectively.
Tickets prices will increase 30 cents for ferries to Bayswater, Birkenhead and Devonport and 50 cents for Northcote Point.
Mr Lambert said public transport remained heavily subsidised in Auckland despite the cost increases.
"Public transport continues to offer good value for money against petrol prices and the full cost of car ownership."
Auckland mayor Len Brown has made an efficient train system central to his vision for Auckland's future.
He is lobbying the Government to invest in a 3.5km-long rail loop around the central city, with a price tag of nearly $3 billion.