The managers of the port - the fifth largest in the world in terms of passenger traffic and the 24th largest in Europe in terms of cargo traffic - say it is one of Europe's cheapest.
With the two parties backing their claims with conflicting data, the ministry has established a joint commission to try to resolve the dispute.
The problem, according to ministerial spokesman Aap Tanav, is straight forward. "The shipowners want to pay less, while the Port of Tallinn wants to earn as much as possible under market conditions," he said.
Enn Kreem, head of the association of Estonian shipowners, highlighted the 20 kroon ($1.12) fee ferry companies are charged per passenger they convey to and from the port. This sum should be halved, he said.
"I would like to hear how they justify these fees. The harbor takes 20 kroons per passenger that passes through the harbor, or 40 kroons for a two-way ticket."
Erik Sakkov, the port authority's marketing manager, said the protest was being driven by Hansatee, the largest of the association's members, which controls 60 percent of passenger traffic. Other companies backing the protest are Eckero Line, Silja Line, Viking Line and Nordic Jetline.
Reducing the passenger conveyance fee to ten kroons would net Hansatee an additional 30 million kroons annually, said Sakkov.
With 6 million passengers passing through Tallinn Port annually, halving the conveyance fee as the association demands would mean the port losing 60 million kroons, he said.
"I'm sure our prices are very competitive, even by comparison with competitors in this region," he said. "We haven't changed our prices for the last seven years and are not planning to change them in the near future. Only the rates for roll-on roll-off cargo can be considered average. Sales by sea transport companies operating in our harbor are worth about $1 billion annually. I don't think it is a sin to earn a cut from such big volumes of trade.
"The shipowners should turn to the government and ask for direct support if money is what they want."
Cargo handling accounts for 55 percent of Tallinn harbor's turnover. Of the 30 million tons which pass through the harbor, two-thirds is for transit to or from a third country, said Sakkov.
Almost every second kroon earned by Tallinn Port is profit. In the first six months of 2001 it earned a profit of 255 million kroons on a turnover of 464.2 million kroons. Most of the profit received last year was paid out in dividends.