The new structure will provide an entry user levy contribution to Nga Maunga Whakahii o Kaipara.
From this week, riders at the country's busiest bike park have to pay an extra $1 for day passes, which had cost $8, and $20 more for annual registration, which was $149. Concession card fees are also amended.
A "development contribution" would also be added to registrations to help with the cost of developing new trails.
Derek Watts, who cycled there with his 9-year-old son yesterday, said he was "not happy" with the increase in charges.
"It was a cheap, good morning's entertainment that I get to do with my son, but with the fees going up I don't know if I'd still be keen," said Mr Watts, a mountain biker for more than 30 years. "It used to be free when the trails were club-operated."
Mr Watts said parts of the bike park still could not be used because of storm damage, so there's no reason why cyclists should be charged more.
However, Bike Parks defended the fee increases and said its registrations still represented exceptional value.
"While we know these changes may not be looked upon favourably by everyone, we need support and understanding as we push forward and build an awesome new mountain bike park over the next three years."
The company said the park has had no external funding or support from councils, charities or grants, and had to rely on support from commercial sponsors.
It said the new agreement would ensure the park's long-term future, and as part of the agreement a new area with "excellent age trees" had been secured for the development of a new trail network.
"This area will provide new challenges and awesome riding terrain for our riding community. This ... will combat the issues surrounding the ongoing harvesting operations within our existing network."
The remaining trails will remain in operation until they are harvested in 2016/17.
Other popular activities at the sand-based pine forest that covers 12,500ha are 4WD and tree-climbing adventures.
Woodhill Forest Bike Park
• Land restored to Nga Maunga Whakahii o Kaipara
• Riders must pay entry levy contribution to iwi
• Increases of between $1 for a day pass and $20 for annual registrations
• New mountain bike park will be built over next three years
• A development contribution will be added to registrations to help with cost.