The Government also announced an additional $5.4 million a year for community-led conservation programmes.
Barry signalled higher fees this year after the Parliamentary Commissioner for the Environment warned that the Department of Conservation needed "a great deal more money".
The Government prefers the users pays fee to a border tax, which has been proposed by the Green Party and is expected to be included in Labour's fiscal plan next week.
Barry also said a "loophole" that allowed international students to book DoC huts without paying would be scrapped.
"Those people will now be charged the full adult rate. A lot of New Zealanders try to book these huts, and then find to their aggravation that school children from Australia or Singapore have booked out the huts for the month of January."
The cost of staying in a hut on the Milford Track would rise to about $140 - a small price for a world-class accommodation, Barry said.
The higher costs were not expected to dent tourist numbers. It was hoped that the higher fees on the more popular tracks would encourage visitors to use some of the less-used Great Walks.
Prime Minister Bill English said the higher fees were not a step towards a tourist levy.
"We just don't need an extra levy at the border. New Zealand is having good tourism growth now but we want to be careful about piling up costs and finding later it's too much."