A new audit of the Department of Energy’s $34 billion loan guarantee program said the agency doesn’t always follows its own rules in awarding the highly coveted funding, creating risk in an effort already hindered by breakdowns.

The audit by the Government Accountability Office carries fresh relevance amid the bankruptcies of two of the first three firms to land the government’s green energy funding: Solyndra Inc. and Beacon Power Corp.

“What we found was problems in how they followed their process and in some cases deviated from the process without a clear explanation why,” Frank Rusco, the GAO auditor who wrote the report, said in an interview. “This has gotten the program in trouble in the past and certainly raises questions that are hard for them to answer.”

The GAO report, the latest to spotlight vulnerabilities in the way DOE awards public money, details just how selective the loan pool is.

Of 460 applicants, the GAO found, the Energy Department awarded loan guarantees to 7 percent and committed to 2 percent more.  To date, the investigative arm of Congress said, the department has issued $15 billion in guarantees and committed to $15 billion more.

The GAO scrutinized 13 winning applications in detail. Of those, it found, the Energy Department did not follow its written procedures at least once in 11 of the 13 cases.

“DOE did not always follow its own process for reviewing applications and documenting its analysis and decisions, potentially increasing the taxpayer’s exposure to financial risk from an applicant’s default,” the GAO found. “It also has not completely documented its analysis and decisions made during reviews, which may undermine applicants’ and the public’s confidence in the legitimacy of its decisions.”

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.

Republicans are calling on Congressional investigators to expand their probe of the Obama Administration’s “green energy” loan program to include Fisker, the start-up electric car company that received more than $500 million in federal support but is assembling its high-end sports sedan in Finland.

“We need to extend the investigation,” Rep. Tim Murphy, a Pennsylvania Republican who sits on the committee that has been investigating the government’s loan program, told ABC News in an interview for "World News" and "Nightline". “If they couldn’t find someone to build the car in the U.S., then don’t do it. Find another way. Find something else.”

Fisker is one of two start-up electric car companies that combined have been offered $1 billion in federal loans through an Energy Department program meant to create jobs and improve air quality through the fledgling alternative energy industry. The loan program has faced intense scrutiny from Congress since the first loan recipient, the solar manufacturing firm Solyndra, declared bankruptcy last month.

A House Energy and Commerce Committee panel has held a series of hearings and released thousands of pages of documents subpoenaed from the Obama administration that showed there were deep divisions about the wisdom of loaning Solyndra $535 million. ABC News reported Thursday that there are now emerging questions about the progress of Fisker Automotive, which has experienced delays with the production of its $97,000 hybrid electric sports sedan. The company has yet to make public even a picture of its next car — a more affordable family car that is supposed to be manufactured in Delaware.