The discovery of a cracked steel beam that forced the abrupt closure Tuesday of the brand-new Transbay Transit Center is the latest headache for the $2.2 billion transportation hub, which has been plagued by glitches and cost overruns since its inception.

The cracked beam was spotted Tuesday morning by workers installing ceiling panels on the center’s third-floor bus platform, and concern over its potential failure prompted city officials to close the terminal and some streets at 4:30 p.m. They shunted rush-hour commuters to the nearby Temporary Transbay Terminal, which had been used during the center’s construction.

The center sits next to the troubled Millennium Tower, which has sunk 18 inches since it opened in 2009. The damaged beam at the transit center was discovered on the same day that engineers inspected a cracked window on the tower, in an attempt to determine if it’s related to building’s sinking and tilting.

The operator of the transit center was quick to give assurances that the two problems were unrelated.

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“We don’t see a nexus,” Transbay Joint Powers Authority Executive Director Mark Zabaneh said at an afternoon news conference announcing the closure.

The transit center is also adjacent to the recently opened Salesforce Tower, the city’s tallest high-rise. Salesforce, the cloud computing company and San Francisco’s largest employer, purchased the naming rights to both the transit center and its rooftop park.

The call to close the transit center and Salesforce Park came on the same day that company founder Marc Benioff was celebrating his birthday and welcoming 170,000 conventioneers to his company’s annual weeklong Dreamforce conference.

While the closure might not have shown those visitors the city in its best light, safety remained the top priority at the center, which opened just 45 days ago after 20 years of planning and almost a decade of construction.

“The beam is cracked, so the behavior of the beam is unpredictable,” Zabaneh said. “We will be working tonight and tomorrow morning to get a better understanding of the cause of the crack.”

The crack is in a 6½-foot-deep American-made steel beam on the third floor near Fremont Street. It’s one of dozens of beams that support the park above the bus deck and is topped by 5 or 6 feet of soil. Late Tuesday evening, the transit authority said it would inspect all steel beams in the center.

The steel was fabricated by Herrick Corp. of Stockton under a $189 million contract with Skanska USA of New York, Transbay Joint Powers Authority documents show.

In a statement released earlier in the day, Zabaneh said the crack appears to be a “localized issue and we have no information that suggests it is widespread.” But he added, “It is our duty to confirm this before we allow public access to the facility.”

The transit center was designed by Pelli Clarke Pelli — the same firm that designed the adjoining Salesforce Tower — and was built by the joint venture of construction companies Webcor and Obayashi.

“We are just beginning work and do not have any information about the cause or causes of the issue at this time,” Webcor said in a statement.

All buses to and from the center were rerouted to the Temporary Transbay Terminal at Howard and Main streets, which was used for the past eight years while the new center was under construction.

Fremont Street, one of the main morning commute arteries off of the Bay Bridge, was also ordered closed to vehicles and pedestrians between Howard and Mission streets, and was to remain closed until at least noon Wednesday. Officials encouraged motorists not to drive downtown.

“Our advice for drivers, if it is at all possible, is to avoid that part of the downtown,” San Francisco Municipal Transportation Agency spokesman Paul Rose said.

The cracked beam is the latest in a series of problems at the center.

It was conceived 17 years ago as the “Grand Central Station of the West,” for buses, trains and high-speed rail — but rail service remains a distant hope, tied up in funding shortages, the uncertainty of California’s high-speed rail project and the logistical challenges of extending Caltrain tracks north from Mission Bay.

Finances have long proved challenging. The center wound up costing $800 million more than expected and required a $260 million bailout from San Francisco to complete its construction.

No sooner did the center open — an opening that was delayed by nine months — than the walkway that circles the nearly three-block-long rooftop park began crumbling.

The shutdown is certain to put pressure on other transit options, but BART officials say they already are operating at full capacity, thanks largely to those 170,000 visitors attending Dreamforce at Moscone Center, where Howard Street is closed between Third and Fourth streets as part of the convention.

“We are maxed out,” said BART spokeswoman Alicia Trost, noting that the district had 613 cars in service Tuesday, compared with the usual 595.

The cracked beam is also reminiscent of the cracked bolts that plagued the eastern span of the Bay Bridge.

“Big projects are increasingly complex,” said Randy Rentschler, spokesman for the Metropolitan Transportation Commission, which helped provide funding for both the bridge and the transit center. “No doubt a full investigation will be completed, and the engineers will get to the bottom of it.”

San Francisco Mayor London Breed declined comment Tuesday, deferring instead to officials at the Transbay Joint Powers Authority.

Supervisor Jane Kim, who sits on the authority and also represents the district at City Hall, said shutting down the building was “absolutely the right thing to do.”

“We cannot put any of our residents or workers at risk,” she said.

Supervisor Aaron Peskin, who has been critical of the project’s high costs, said he hoped the problem was a “one-off.”

“They still owe us a quarter of a billion dollars,” Peskin said. “Happy Transit Week.”

Chronicle staff writer Kurtis Alexander contributed to this story.

San Francisco Chronicle columnists Phillip Matier and Andrew Ross appear Sundays, Mondays and Wednesdays. Matier can be seen on the KPIX TV morning and evening news. He can also be heard on KCBS radio Monday through Friday at 7:50 a.m. and 5:50 p.m. Got a tip? Call 415-777-8815, or email matierandross@sfchronicle.com. Twitter: @matierandross