He said there was significant community interest in visiting ships and the shipping guide was also used by customers and shipping agents. The online shipping guide received more than 4000 visits a week.
"Napier Port is a vital part of the Hawke's Bay community however, it is worth remembering it is a commercial entity and our customers are critical to our business."
Mr Cowie did not respond to a request to identify past unlisted visits.
Auckland Port was more forthcoming, saying unlisted requests granted in the past have been from "a few" superyachts and last year, during the Navy's 75th anniversary, for the arrival of a United States Navy ship.
"We haven't done it for any freight ships," a spokesman said.
Lyttleton Port refused to say if it had unlisted visits, in case its reply affected the perception of Napier Port.
"It's not appropriate for Lyttleton Port Company to comment on matters relating to other ports, so the port won't be making a comment on this one," a spokesman said.
Wellington's Centreport and Port of Tauranga did not respond to a request asking if they did not publish all ship visits.
Napier Port services manager Bruce Lochhead said it was the "right" of the shipping agent to request it not be included in the shipping guide.
Napier Port chairman Alasdair MacLeod said he was unaware of the port's practice of not listing ships.
The request to not include Ocean Drover, the world's largest livestock carrier, from last week shipping guide was made by the shipping line.
Live exports is a controversial practice following past disasters. In 2003 thousands of sheep died on their way to the Middle East from New Zealand, resulting in a ban on live sheep exports.
The 3000 heifers loaded in Napier on to Ocean Drover joined the same number loaded on to the ship in Timaru. All are bound for Fonterra farms in China.
A Fonterra spokesperson said the Holstein-Friesians received a changed diet "well in advance" of boarding but could not explain how a claimed "special transition programme" accustomed them to the ship environment.