The Port of New York and New Jersey ground to a halt Friday after members of the International Longshoremen’s Association staged a surprise walkout, only to reopen about nine hours later after emergency negotiations with the port’s leading shipping association.

John Nardi, president of the New York Shipping Association, which negotiates the union’s contract with port management, said work would resume at the port’s terminals starting with the 7 p.m. shift Friday. Terminal gates are typically closed to trucks on weekends, but some union dockworkers unload vessels and do other work at the ports on Saturday and Sunday.

The Port Authority of New York and New Jersey said it expected all its container terminals to open on schedule Monday morning with full service resuming.

ILA members either halted work or left the terminal facilities starting around 10 a.m. at all six of the port’s marine terminals, effectively closing the East Coast’s busiest seaport.

The terminals import and export more containers than any U.S. port outside of Los Angeles and Long Beach, and even a brief shutdown can disrupt commerce across the region. More than 3 million containers pass through the Port of New York & New Jersey each year. It is a key entry point for consumer goods, automobiles and building supplies, among other products, which in 2014 were worth more than $200 billion.

By Friday afternoon, more than one thousand trucks were sitting idle at or near the terminals, according to Jeff Bader, president of the Association of Bi-State Motor Carriers, which represents port trucking companies.

“Right now the entire economy of the port is shut down,” Mr. Bader said. “We’re pulling all our trucks in and we’re heading home. We’ve missed hundreds and hundreds of exports. Containers are sitting there unmoved. You’re talking about hundreds and hundreds of thousands of dollars this thing has cost us.”

ILA spokesman Jim McNamara said the walkout was a unified action against the Waterfront Commission of New York Harbor, a bistate body that investigates corruption and regulates hiring practices among dockworkers. Longshoremen said the commission had interfered in hiring and the union’s collective bargaining agreement with the New York Shipping Association, and was “jeopardizing the future of the industry with this interference,” he said.

Mr. Nardi said the walkout was illegal because it violated clauses in the union’s contract with port management preventing most unplanned work stoppages. The NYSA called called an emergency meeting of its contract board, which includes union representatives, at 3 p.m. Friday afternoon, but initially couldn’t reach an agreement to restart work. Around 4 p.m., the NYSA met with an arbitration panel, which ruled in the shipping association’s favor. The NYSA was preparing to seek a court injunction to force the longshoremen back on the job when negotiations resumed, an a deal was struck around 6 p.m. Friday.

Truckers and terminal operators said the work stoppage came without warning. Mr. Bader said at least 18 drivers with his company, Golden Carriers Inc., were stranded on the piers at the port, and that ILA clerks, who coordinate the movement of cargo from ships to trucks ashore had stopped working at all terminals.

The Waterfront Commission declined to comment on its role in prompting the work stoppages, but denied that it is interfering with port commerce. “If anything, the Waterfront Commission is carrying out its statutory mandate to require fair and nondiscriminatory hiring at the port, which is a marked departure from what had occurred in prior years,” said Ronald Goldstock, the agency’s New York commissioner.

The ILA has clashed with the Waterfront Commission for decades, but tensions have come to a head recently. The union, along with NYSA, sued the commission over a 2013 decision to expand hiring regulations aimed at eliminating hiring practices that the commission says were discriminatory. The Waterfront Commission won that case in a district court, but the two parties clashed in federal appeals court in August. The case awaits a decision from the court, which is expected this year.

In addition, on Wednesday, state lawmakers in New Jersey introduced a bill into the state legislature calling for the governor to withdraw from the compact establishing the Waterfront Commission, thereby dissolving it and transferring its New Jersey operations to the New Jersey State Police.

Mr. McNamara, the union spokesman, said that the Waterfront Commission had targeted certain ILA members with “harassment” since the bill was introduced, but insisted that the walkout was organized by union members, and not ILA leadership.

In an emailed statement, the Port Authority of New York & New Jersey, the bistate agency that oversees the port, urged ILA members Friday afternoon to return to work immediately. and resolve their differences after they return.”

A major retail trade group said late Friday that a prolonged strike at the port “could could hamper economic growth and wreak havoc on spring deliveries,” and called for the parties to resolve the walkout quickly.

“This is déjà vu for retailers, and an unwelcome start to 2016,” said Kelly Kolb, vice president of government affairs for the Retail Industry Leaders Association, referring to a labor dispute in late 2014 and early 2015 that led to prolonged delays at West Coast ports. “A long-lasting strike would ultimately impact thousands of jobs along America’s supply chain.”