Leroy Beckett of the youth-led group lobby Generation Zero said the documents "effectively confirmed" rail would not be part of the crossing and so his organisation was calling for a rail connection to be at the top of the agenda for the local election.
In an NZTA paper from November 2014, one of the key issues was that there was no rail on the North Shore so Auckland Transport's support for protecting the route for rail "now is unclear".
However, a briefing document three months later said the business case to be completed next year would consider rapid transit options.
Mr Bridges believed the Transport Blog and Generation Zero had misinterpreted the documents and said the Transport Agency was using the term "rapid transit" in its plans for the crossing so it didn't corner itself into using only rail rather than keeping its options open.
"I'm absolutely certain the second harbour crossing will need rapid transit of some form and it may be rail, but there's so many other options which will be tried and true by 2025," the minister said.
Mr Bridges said he was surprised by Generation Zero's position on rail instead of looking at more innovative public transport options that were around the corner, such as autonomous buses.
"Rather than defaulting to rail technologies used since the 1860s, you'd hope that Gen Zero would be advocating for other options to be considered."
An NZTA spokeswoman said the agency could designate only for the road component of the crossing and was working with Auckland Transport on ensuring the design was future-proofed and enabled a public transport crossing option.
"While we don't yet know when it will be required, and precisely what form it will take, in a rapidly growing region it's essential that we protect and keep future transport options open."
Auckland Transport's chief strategy officer, Peter Clark, said the Northern Busway serving the suburbs north of the bridge had been a huge success and one of the benefits of another crossing would be to continue it across the harbour.
It could then also be used for rail or other innovative public transport options in future, he said.
In 2008, after looking at 159 options, a partnership identified an additional Waitemata Harbour crossing, operated in conjunction with the existing Auckland Harbour Bridge, as the most appropriate solution to provide flexibility, resilience and sustainability for the city's expected growth.
Together, the crossings would provide 14 lanes for general traffic, public transport, walking and cycling.
The next steps for the project involve working with consultants to prepare Notices of Requirement, which would designate the land required, and preparing a detailed business case to look at what the timeframes will be and weighing funding options.
