Mr Lee, who led North Island regional leaders in a successful 2006 campaign to save the former Overlander service between Auckland and Wellington from extinction, said long-distance trains needed to connect with Metro rail operations.
"Britomart is absolutely vital for encouraging tourists and Aucklanders to use rail for long-distance travel," he said.
Public Transport Users Association co-ordinator Jon Reeves accused KiwiRail of putting the Northern Express "in a choke hold and waiting for it to faint".
"The old Auckland railway station [off Beach Rd] was never a success for 80 years in operation, and essentially they are putting it back there," he said.
"It's very inconvenient for people carrying baggage to find themselves in the middle of nowhere - it's a very industrial area with no decent transport links."
Mr Rutherford described Mr Lee's comparison as "a little bit unfair" and said KiwiRail would run a coach shuttle over the 1km between Britomart and the previously little-used Strand Station, which Auckland Transport upgraded for $2 million for emergency Rugby World Cup rail duties in 2011.
He said KiwiRail was proud of patronage growth on the thrice weekly Northern Explorer service - which rose 22 per cent to 39,419 passengers in the year to June 30 - and had no intention of running it down.
It was making the move before changes to Britomart next year to accommodate Auckland's $2.5 billion underground rail extension.
It meant the 12-year-old station's diesel ventilation system would not need upgrading, as the removal of the Northern Explorer would leave it for the exclusive use of new electric trains.
Despite an expected cost of under $200,000 for modifying the containers, Mr Rutherford said they would have a modern look consistent with tourist expectations.
It would be a distinctly KiwiRail Scenic Journeys terminal and departing trains could park for 45 minutes, allowing plenty of time to board without interrupting Metro rail services.
