Lee, the Waitemata and Gulf ward councillor, said part of the problem was that the price Ports of Auckland received for processing containers was "significantly lower" than that received by Australian ports.
"That is simply because [of] the astute manipulation by the shipping cartel Maersk and the major shipper Fonterra," Lee said.
"They've been able to keep the price right down by playing Tauranga off with Auckland."
An Auckland Regional Holdings study released in 2009 said Australian ports received on average about 50 per cent more for processing a container than their New Zealand counterparts.
Lee said there was a "race to the bottom" in container pricing between Auckland and Tauranga, which did not benefit the shareholders of either port.
The two companies should collaborate and get a higher rate per container.
"It seems to me that Tauranga and Auckland need to get together, because they are both cutting each other's throats economically, and get a world-market price for processing containers," he said.
However, Port of Tauranga chief executive Mark Cairns said this would require a merger between the two companies, an option neither port was considering.
A Ports of Auckland spokesperson echoed this comment.
Cairns also did not think the price New Zealand ports received for processing containers was behind Auckland's problems.
"We're meeting our cost of capital at those rates, so I don't think the revenue line is the issue. It's that costs are blown and that is something [Ports of Auckland chief executive] Tony Gibson is working on addressing."
Moreover, Cairns said, when comparing prices received per container with the prices fetched in Asian ports, Australian rather than New Zealand ports were the outliers.
Although competition between Tauranga and Auckland is fierce, the possibility of a merger has been raised a number of times.
In 2006, the two parties worked together on a merger proposal, but this was dropped a year later.
Although Gibson said last week that keeping the two entities separate encouraged competition, Cairns said the failure of the 2006 proposal was a "lost opportunity".