Correction: An earlier version of this article incorrectly said that Ener1, a company that makes lithium ion batteries, had received an Energy Department loan guarantee. It was Ener1’s parent company that received the federal support, and it was an Energy Department grant.

Blue flywheel battery pits are seen at Beacon Power in Stephentown, N.Y., on Thursday, July 7, 2011. (AP Photo/Mike Groll))

In August 2010, Beacon Power became one of the first companies in the nation to get an Energy Department loan guarantee designed to jump-start innovative and clean energy projects. On Monday, it became the second one to file for bankruptcy.

Beacon Power — which uses large flywheels to store power and help grid operators smooth out dangerous electrical surges — owes the Energy Department $39.1 million and the state of Massachusetts $3.45 million. Its technology was considered a promising way to ensure grid reliability, especially as fluctuating wind and solar energy sources come online.

The company has a 20-megawatt facility in Stephentown, N.Y., east of Albany. In a Sept. 15 presentation, Beacon chief executive Bill Capp said the facility had been “highlighted by the White House as one of the 100 Recovery Act projects that are changing America.”

But the company failed to attract investors. Its revenues were tiny. A problem in July with one of its 200 flywheels in Stephentown fanned investor concerns about maintenance costs. A ruling by the Federal Energy Regulatory Commission on Oct. 21 might have doubled or tripled Beacon revenues by rewarding its speedy response time, according to Capp. But analysts said it was too little, too late.

“It’s a good technology,” said Walter Nasde, an analyst at Ardour Capital. “But the question is, is this something you can build a business around?”

The company’s shares, which traded for as much at $47 .40 in 2005, were down to $3.44 at the end of February and recently slid below $1 a share, prompting Nasdaq to notify Beacon that it would delist the company. Beacon’s shares closed Monday at 10.7 cents a share, down 80 percent in five days, giving the company a market value of $3 million.

Beacon raised money for its New York plant thanks to the same loan guarantee program that provided funds to Solyndra, the solar panel manufacturer that went bankrupt with $535 million in guarantees two months ago. Solyndra has been the center of controversy over whether the Energy Department adequately assessed the company’s risks and whether Solyndra benefitted from any connections to the Obama administration.

Unlike Solyndra, Beacon Power has a fully operating facility that is generating revenue, which could help the Energy Department recover some of its $39.1 million loan guarantee.

“Protecting taxpayer dollars remains the top priority,” Energy Department spokesman Damien LaVera said in an e-mail. He said that the loan guarantee was given to the Stephentown project and that “the loan was set up in a way that ensures the Department is not directly exposed to the liabilities of the parent company.”

He added that the Stephentown plant “is a valuable collateral asset” and that the subsidiary “has cash reserves and proceeds from the plant that it was required to hold as collateral on the loan.” He said the Energy Department is “the only senior, secured lender of the Stephentown project company, which owns the plant.”

Beacon Power’s revenues from the plant were $525,000 in the second quarter of 2011.

Capp, Beacon’s CEO, has promoted renewable energy in Washington political circles, visiting Capitol Hill as recently as mid-September. He is a member of Environmental Entrepreneurs, a group that advocates clean energy technology.

In an interview Sept. 14, Capp said his company would not have been able to construct its Stephentown plant without federal assistance.

“We absolutely couldn’t have done it without support from the government, because no one else was willing to do it,” he said, adding that it was challenging to find venture capital firms willing to finance a plant. “The projects are so huge, that’s the problem. If you demonstrate an energy technology on a grid scale, that’s $100 million.”

Capp added that he didn’t understand the political furor surrounding Solyndra’s collapse.

“I don’t get it. The whole point of the loan guarantee program is it was designed to help companies that weren’t quite ready to get a commercial loan,” he said.

Beacon also won a $24 million Energy Department grant to build a new facility in Hazle Township in northeast Pennsylvania but has spent less than $1 million of the grant, which required the company to find matching funding.

Separately, the Energy Department’s Advanced Research Projects Agency-Energy approved $2.2 million for Beacon research. About a third of that has been spent.

Perseus LLC, a District-based venture capital firm, was one of Beacon’s primary investors. When asked for comment, a Perseus employee who did not identify herself said: “We do not talk to the media.”

Nicole Lederer, co-founder of Environmental Entrepreneurs, said she viewed Beacon’s product as “an integral and key component to driving this country toward a more self-driven, self-reliant energy system.”

She said that federal support was important. “This country is not doing nearly enough to help this industry get off the runway and into the air,” she said.