BRADENTON, Fla. — After hours of wrestling over which financing option was least likely to provoke a third investigation by the Securities and Exchange Commission, city of Miami officials chose a limited public offering to refinance a bank loan Thursday.

The $45 million loan with Wells Fargo Bank NA was obtained nearly two years ago to finance a portion of the city’s cost of the Port Miami tunnel project to divert traffic from downtown to nearby major highways. The loan matures in January.

Commissioner Francis Suarez, chairman of the board, repeatedly questioned which of two proposals would cost the least in potential legal fees if there was an SEC inquiry.

The city’s finance team recommended Wells Fargo to underwrite a limited public offering to qualified institutional investors over a private equity option proposed by Ohio-based Gates Group Capital Partners based on a lease-back arrangement that could be sold to real estate investors.

The cost difference between the two was estimated to be $4.39 million over the 18-year life of the limited public offering, or $1.79 million in present value, according to David Moore, managing director at Public Financial Management Inc., the city’s financial advisor.

Commissioners discussed at length the costs, if one proposal would require less disclosure than the other, and which deal could bring SEC scrutiny to the city once again.

Graham White, chief investment officer at Gates, told commissioners his firm’s proposal would not require disclosure to the SEC or investors.

Suarez, weighing the cost differences, said the city has already spent several million on two SEC investigations, the city’s rating is on watch for possible downgrade, and Miami declared a “financial urgency” to get union concessions and close a budget gap for fiscal 2013.

“No one can guarantee there will not be an SEC investigation on anything,” said Albert del Castillo, a partner at Squire, Sanders & Dempsey LLP, the city’s bond counsel.

Long deliberations will not “engender a terrific amount of confidence,” del Castillo told commissioners, adding that it could accelerate an SEC investigation.

The SEC is considering sanctions for alleged securities violations believed to be based on failure to disclose budget problems in bond documents for three offerings between 2007 and 2009.

Last December, the SEC launched a second investigation into the public and private financing of the $634 million retractable-roof stadium built for Major League Baseball’s Miami Marlins.

A Wells Fargo representative told commissioners that a great deal of time has been spent developing disclosure documents, and that due diligence has “advanced quite far” on the limited public offering. The bank believes there will be no problem issuing bonds, and closing can occur in early December, the representative said.

Commissioner Marc Sarnoff said that both financing options were viable, and calculating the liability with either one was a difficult task.

“There is a risk involved but I think it’s a manageable risk,” he said, supporting the limited public offering recommended by the city’s finance experts.

The commission voted unanimously for the public financing option, and an interlocal agreement requiring the Omni Community Redevelopment Agency pay to debt service associated with the limited public offering.

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