Duke Energy will permanently close its Crystal River Nuclear Plant in Florida, which has been out of commission since 2009, after botched repairs.

Charlotte, NC-based Duke Energy said it is starting a closing process that may take 60 years before the nuclear site ends up decontaminated and dismantled. In addition, the largest utility in the country said it is weighing whether to build a new, natural-gas-fueled power plant to replace the power lost.

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Duke said it will return to customers $835 million from an insurance settlement because they had to pay for higher-cost replacement power. But Duke also said it will seek to recoup from customers its $1.65 billion investment in the plant, 70 miles north of Tampa.

The nuclear plant, operated by Duke Energy subsidiary Progress Energy Florida, shut down when its concrete containment building cracked during a maintenance and upgrade project. A 2011 repair attempt resulted in new cracks in other parts of the containment structure. Estimates put repair costs at between $1.3 billion and $3.4 billion.

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The federal license for the nuclear plant, which began operating in 1977, was due to expire at the end of 2016, meaning Duke Energy would have had to wage a regulatory fight to extend its authority to operate.

“We believe the decision to retire the nuclear plant is in the best overall interests of our customers, investors, the state of Florida and our company,” said Duke Energy Chairman and Chief Executive Jim Rogers.

Rogers’ expected successor following Duke Energy’s merger last July with Raleigh-based Progress Energy, which owned Crystal River, ended up unexpectedly fired within hours after the merger was complete. Duke Energy board members said they dumped Progress Energy Chief Executive Bill Johnson in part because of dissatisfaction over his handling of the Crystal River project.

Duke Energy said in a filing with the Securities and Exchange Commission that it would seek to recover its investment in Crystal River over a 20-year period beginning in 2017, an amount spokesman Mike Hughes said was $1.65 billion.

Progress Energy Florida provides electricity to more than 1.6 million Florida customers, including the cities of St. Petersburg and Clearwater and the area surrounding Orlando.

Florida Public Counsel J.R. Kelly called the company’s decision a bad one for consumers, who face the potential of higher rates to pay for more expensive alternate power sources. The settlement of Duke Energy’s dispute with its insurer, Nuclear Electric Insurance, shortchanged ratepayers because the additional $530 million NEIL agreed to pay was less than half the lowest projected repair cost, said Jon Moyle Jr., a lawyer for the Florida Industrial Power Users Group, which advocates for manufacturers.

Florida utilities regulators will decide when customers see refunds to compensate for higher bills Progress Energy passed along because it had to replace electricity not produced by the nuclear plant with higher-priced power.

Florida’s Public Service Commission last February allowed a $150 million increase in base rates but directed Progress Energy Florida to refund customers $288 million over two years for costs related to the nuclear plant shutdown. That money ended up included last month, Mike Hughes said. Another $100 million is due to customers in 2015 and 2016 because repairs on Crystal River had not begun by the end of 2012.

Duke Energy spent $338 million through the end of 2012 to repair the nuclear plant, $143 million of which insurance payments covered. Florida regulators will determine how much of the cost to close the plant customers will cover or end up absorbed by shareholders, Hughes said.

“The ultimate allocation of those costs will be determined in the future, so I don’t have any specific percentage that we anticipate that customers might pay, a specific percentage that we anticipate shareholders might pay. That will be determined by the proceedings” convened by state regulators, Hughes said.

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