The New York Shipping Association said it will cut its staff by a third over the next three months, with cuts accompanying a reconfiguration of its computer system and qualified employees being offered early retirement.

The NYSA represents management at the Port of New York and New Jersey. It negotiates contracts with organized labor in the port and collects a tonnage assessment levied on port cargo to pay dockworkers' fringe benefits.About 30 of the NYSA's 90 employees will be lost. Of the 90, around 40 percent are involved in management information services.

"Today's dismal economic conditions demand that we take every possible step to increase efficiency and reduce costs," James A. Capo, NYSA president, said in a written statement. "This is a difficult decision, but it's the only one we could responsibly make."

The NYSA has imposed a pay freeze for the past nine months or so and computer staff has been falling gradually over the last few years.

Mr. Capo, who stepped into the president role a year ago from a position outside the maritime industry, has pledged to make the NYSA as efficient as possible.

When the association was searching for a new president, sources said it was going to look outside the maritime industry to find someone with a high level of managerial skill and with professional experience in labor relations.

The NYSA's labor contract with the International Longshoremen's Association does not expire until the fall of 1994. Dockworkers now earn $20 an hour.