President Obama’s Department of Energy financed a fleet of green energy companies that later fell into bankruptcy — but not before the firms doled out six-figure bonuses and payouts to top executives, a Center for Public Integrity and ABC News investigation found.

Take, for instance, Beacon Power Corp., the second recipient of an Energy Department loan guarantee in 2009. In March 2010, the Massachusetts energy storage company paid cash bonuses of $259,285 to three executives in part due to progress made on the $43 million energy loan, Securities and Exchange Commission records show. Last October, Beacon Power filed for Chapter 11 bankruptcy.

Ener1 subsidiary EnerDel, maker of lithium-ion battery systems, landed a $118.5 million energy grant in August 2009. About one-and-a-half years later, Vice President Joe Biden toured a company plant in Indiana and heralded its taxpayer-supported expansion as one of the “100 Recovery Act Projects That Are Changing America.”

Two months after Biden’s visit, corporate parent Ener1 paid $725,000 in bonuses to three executives — including $450,000 to then-CEO Charles Gassenheimer, who led Biden on the tour. This January, Ener1 filed for Chapter 11 bankruptcy protection.

At least two other firms that benefited from Energy Department funding — one a $500,000 grant, the other a $535 million loan guarantee — handed out hefty payouts to executives and later went bankrupt.

The Department of Energy, asked about the payments examined by the Center and ABC, said it is troubled by the practice and intends to convey that message to loan recipients.

A politically connected solar company that pocketed a half billion dollar government loan, only to shutter its doors, fire workers and file for bankruptcy, secured an interest rate lower than other green energy projects, iWatch News and ABC News found -- one in a string of benefits the Obama administration doled out in bankrolling the project.

Now, the government’s agreement with the company compels taxpayers to take a back seat to a venture fund associated with a key Obama fundraiser in trying to collect on the debt. Investors who put in $75 million would be repaid first; some $150 million of the government's $535 million would be next in line, according to the Energy Department's agreement with the company.

The $535 million loan to Solyndra Inc., issued by the Treasury Department's Federal Financing Bank as part of the Obama administration’s stimulus to create jobs and spur development of green energy, included a quarterly interest rate of 1.025 percent, the government bank reported in July. Of 18 Energy Department stimulus loans cited in the bank’s report, Solyndra’s rate was lowest. Eight other Energy Department projects, each also backed by the Federal Financing Bank, came with rates three or four times higher, the report shows.

A Department of Energy loan program, infused with $25 billion to spur a wave of fuel-efficient vehicles, has not closed a loan in two years and is likely to leave two-thirds of the money unspent amid fallout over the Solyndra debacle and other factors.

Those findings, revealed Friday in a U.S. Government Accountability Office report, rekindle questions over how effectively the Energy Department picks winners and losers for its lucrative green energy portfolio.

The audit focuses on DOE loan programs, including one known as ATVM — the Advanced Technology Vehicles Manufacturing program.

That program was pitched as part of a broader government campaign to spur innovative, clean technologies that would both rev up the economy and clean the environment. Under ATVM, the government would help bankroll electric cars and other fuel-saving initiatives; this seed money would, in turn, trigger a domino effect for industry and consumers.

Yet the last loan closed in March 2011, and just $8.4 billion has been spent so far in five projects.

The money, records show, helped stalwarts Ford Motor Co. and Nissan North America transform factories to build fuel-efficient vehicles, and cutting-edge upstarts Tesla Motors and Fisker Automotive develop electric cars and plug-in hybrids. A smaller loan went to a Miami company to develop wheelchair-accessible vehicles to run on compressed natural gas.

Yet not all the projects have found success.

They are two cutting-edge electric car makers, headquartered in California and backed by powerhouses of politics and money. In 2009, each secured half-billion dollar loan commitments from President Obama’s Department of Energy to help transform their clean-energy cars from drawing boards to showrooms.

But this week, the fortunes of Tesla Motors and Fisker Automotive took sharply divergent turns.

On Wednesday, the Energy Department announced that Tesla repaid the balance of its $465 million government loan nine years early. Fisker, meantime, has ceased making cars as it weighs potential bankruptcy, confronts a $171 million loan balance with DOE and, last month, faced questions from the House Committee on Oversight & Government Reform.

In October 2011, The Center for Public Integrity and ABC News explored the Energy Department’s risky $1 billion bet on two companies lauded for their innovative design, but facing warnings from experts over the marketability of cars that, in some models, carry price tags hovering around six figures.

In announcing Tesla’s loan repayment this week, the department said the risks were worth taking, coming at a time the industry itself suffered a deep downturn. “The lack of financing for the automotive industry was critical and potentially lethal,” Energy Secretary Ernest Moniz said in a statement. “Providing these loans was a calculated risk — but it was the right decision for the country.”

NEW YORK — The Center for Public Integrity and ABC News were awarded an Emmy Award Monday for their yearlong investigation exposing flaws in a U.S. government green energy program meant to boost new and innovative technologies.

Center senior investigative reporter Ronnie Greene and a team from ABC were honored for Green Energy: Contracts, Connections and the Collapse of Solyndra, a series of reports exploring  how the Department of Energy awarded lucrative green energy contracts. The coverage detailed breakdowns in the award to solar panel maker Solyndra Inc., which later filed for bankruptcy, and examined connections between Obama campaign bundlers and the DOE.

The prestigious News & Documentary Emmy Awards, presented Monday at Lincoln Center's Rose Hall, honored the Center and ABC for Outstanding Business and Economic Reporting. The ABC team included producer Matthew Mosk and chief investigative reporter Brian Ross.

Click here to read ABC’s story. Watch the segment by ABC World News with Diane Sawyer here.