SAN FRANCISCO (CBS SF) — The sinking and tilting of Millennium Tower has raised new questions about San Francisco’s downtown building boom.

Now San Francisco officials may be putting the brakes on one of its biggest projects ever over uncertainty about whether it is safe to move forward with the massive Transbay Terminal tunnel project.

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The project would extend Caltrain tracks between the Transbay Terminal and AT&T Park and eventually bring bullet trains to the new terminal.

Nearly $6.8 million in funding for the second phase of the Transbay Transit Center project was put on hold this week as supervisors demanded more information about potential costs and liability from the sinking Millennium Tower.

San Francisco supervisors, acting as the San Francisco County Transportation Authority board, voted 7 to 3 Tuesday to withhold nearly $6.8 million in Proposition K sales tax funding for design work on the transit center’s second phase.

San Francisco’s skyline is growing like never before with even more skyscraper construction planned.

But concerns over Millennium Tower now have San Francisco Mayor Ed Lee asking questions about the new high rise development and the underground rail tunnel being proposed for the downtown.

“Is this going to be safe?  Will it be safe in the event of an earthquake?” asked Lee.

That concern has prompted the mayor to call for an independent review of building codes for current and future high rises in the downtown.

“Not only what do we do now, but what do we do in the future for all of these developments that are in that mud area?” wondered Lee.

That landfill area that makes up a good portion of the South Beach neighborhood is now some of the most expensive real estate in the country.

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“Where we are standing used to be on under water so, as we continue thought this building boom, let’s make sure we are doing it right,” said San Francisco Supervisor Aaron Peskin.

The call for an independent investigation comes after weeks of finger pointing over how city’s building department cleared the 58-story Millennium Tower for construction only to have it wind up sinking some 16 inches and counting.

“I think everyone is afraid of accepting the risk,” said Lee. “Well, I’ve got the bigger risk, I think, as a city. And as a mayor I want make sure that we handle this.”

The concerns about the stability of the area extend beyond possible issues the continuing construction could cause.

“I’m concerned about the area being able to withstand a major earthquake, and that is what we need to build toward a standard for,” said Lee.

One immediate result: the board of supervisors are withholding money on plans to build a massive underground train tunnel between the Transbay Terminal and the South of Market.

“We want to put the brakes on this thing and make sure that we are doing it right before we move forward,” said Peskin.

Others disagree, saying that is an overreaction.

“We had a big earthquake in 1989 and they held up fine,” said Supervisor Scott Wiener. “I don’t we should overreact because Millennium Tower has a problem; that we should stop everything in its tracks.”

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The board is expected to review the funding issue again after obtaining more information from authority officials at a meeting next month.