Top executives at Fannie Mae and Freddie Mac were paid handsomely in the last two years, while the government agency in charge of regulating the bailed-out mortgage backers was ill-equipped to do anything about it, according to a federal review.

The inspector general for the Federal Housing Finance Agency  said the top six executives at Fannie and Freddie received a combined $35.4 million in 2009 and 2010, while the companies were in federal receivership.

Of that, both chief executives were paid $17 million, according to the report. If they had met their performance targets, the CEOs would have received a combined $24 million over two years.

The chief executive of Freddie Mac is Charles “Ed” Haldeman; Michael Williams is in charge at Fannie Mae. Both were appointed in 2009.

Representatives for Fannie and Freddie declined to comment on the report.

Fannie and Freddie are government-sponsored enterprises, or GSEs, that buy home loans that meet certain standards and convert them into assets that can be sold to investors. They stand behind the vast majority of mortgages in the United States.

The institutions, which were publicly traded at one time, were rescued by the government in 2008 as the downturn in the housing market led to staggering losses on bad loans. The two have received more than $150 billion in taxpayer aid since then.

Congress is debating ways to wind down Fannie and Freddie, which represent a major liability for U.S. taxpayers, and reduce the government’s role in the mortgage market without raising costs for low-income borrowers.

Steve Linick, the inspector general, said the Federal Housing Finance Agency has a responsibility to “efficiently, consistently and reliably ensure that the compensation paid to Fannie Mae’s and Freddie Mac’s senior executives is reasonable.”

“This is especially true when you realize that the U.S. Treasury has invested close to $154 billion to stabilize Fannie Mae and Freddie Mac, and the GSEs are spending tens of millions of dollars for executive compensation,” Linick said.

The inspector general found that agency did not review the issues necessary to determine whether compensation practices at Fannie and Freddie were “reasonable” and sufficient to “recruit and retain key professionals.”

He also said the agency lacks “key controls” to monitor the ongoing compensation decisions under the companies’ approved packages. In addition, the report faults financing agency for a lack of transparency in its disclosures of compensation policies at Fannie and Freddie.

A spokeswoman for agency did not immediately respond to a request for comment. But in testimony before Congress Thursday, the agency’s acting director, Edward DeMarco, said overall compensation at Fannie and Freddie has been reduced by 40 percent since the companies were taken over by the government.

“Retaining human capital in the face of a very uncertain future is a difficult task and setting a compensation strategy in such an environment requires a delicate balancing act,” he told members of the House Financial Services subcommittee on capital markets, insurance and government-sponsored enterprises.

DeMarco testified that the agency has directed Fannie and Freddie to keep 2011 compensation at last year’s level, which he said was the lowest in 12 years.

“FHFA is very mindful of keeping enterprise compensation costs down, while retaining the talent to carry out the operations of the companies,” he said.