The Obama administration approved “excessive” pay for top executives at General Motors Co. and Ally Financial Inc. even as the two companies were falling behind on repaying taxpayers for being rescued after the Wall Street collapse, the bailout watchdog concluded in a report released Wednesday.

In a scathing rebuke, the special inspector general that oversees Troubled Asset Relief Program spending said the Treasury Department’s office of the special master — also known as the pay czar — is ignoring President Obama’s own stated goal of limiting salaries for executives of companies that took bailouts.

Eleven executives of Ally, the onetime financing arm of the country’s biggest automaker, made at least $1 million more than comparable executives at similar companies, the inspector general said. The inspector general said not only does that suggest poor priorities for taxpayers’ money, it warned that higher payments could contribute to the same short-term financial thinking that caused the 2008 Wall Street collapse in the first place.

“The pendulum in OSM’s pay decisions has swung too far in the direction of keeping companies competitive, without regard for the fact that the reason to keep companies competitive is so that they can repay taxpayers in full,” investigators concluded. “But GM and Ally were not repaying taxpayers in full. Rather, taxpayers have suffered billions of dollars in losses on those TARP investments.”

Their report serves as a particular admonishment for Mr. Obama, who campaigned on corporate accountability, promised to crack down on the bad actors who spawned the Wall Street crash and specifically called for limits to salaries of executives from companies that took part in the bailout.

Mr. Obama in 2009 famously criticized bailed-out companies for refusing to ease credit for troubled borrowers in the wake of the bailouts, saying, “I did not run for office to be helping out a bunch of fat cat bankers on Wall Street.”

Treasury Department officials, in their response to the report, said they believe they are following the law. They also argued that, overall, the federal government has recovered all of the taxpayers’ money used to bail out the seven companies aided in the wake of the collapse: American International Group, Bank of America, Chrysler LLC, Chrysler Financial and Citigroup, in addition to Ally Financial and GM.

Six of the companies have been released from TARP oversight, leaving only Ally and its executives’ pay under scrutiny of the Treasury Department.

“Pay packages for the top 25 employees at each of those companies have been restricted so long as the company remained in TARP. Only one of the seven companies remains under OSM’s jurisdiction, and taxpayers have recovered $25 billion more than was originally invested in the companies,” said Special Master Patricia Geoghegan, the pay czar.

She said the inspector general’s report “unfortunately contains many inaccuracies and omissions.”

Mr. Obama had called for executives’ cash salaries to be limited to $500,000. The inspector general reported on nine GM and six Ally executives in 2013 whose cash pay exceeded that level.

When stock options were added in, the inspector general found one Ally executive was paid more than $5.6 million, while the median market pay for that position was just under $3 million.

All told, auditors listed 30 employees across the two companies who were overpaid in 2013 to the tune of $22 million.

Beyond the dollar amount, the investigators said the Treasury Department was approving compensation packages that rewarded riskier corporate behavior.

In the case of Ally, the pay czar in 2013 gave only “a tiny” portion of pay in long-term restricted stock tied to long-term corporate success. There was no bother with any such compensation in 2014, the investigators said in the report.

“Eroding reforms coming out of the financial crisis could have the dangerous effect of allowing companies to end up in the same place that required reforms in the first place,” the inspector general said. “Should this nation face the possibility of a future bailout, strong limitations on executive compensation on this still-existing TARP bailout could have a deterrent effect on companies asking the government for federal dollars. No one employee, no matter how valuable to his or her company, is important enough to risk weakening a deterrent to future bailouts.”

The inspector general and Ms. Geoghegan traded statistics and calculations for executive pay in justifying their decisions and conclusions.

The inspector general said both Ally and GM were in arrears to taxpayers — GM to the tune of $8.2 billion at the time of the 2013 pay decisions. The Treasury Department disputed those calculations, though, saying that when stock sales were included, the seven special bailout cases took $352 billion in total assistance and have returned $25.5 billion more than that to the government’s coffers.

For Ally specifically, the government invested $17.2 billion and has gotten back $650 million more than that. The government’s remaining shares in Ally are also valued at nearly $1.8 billion, the Treasury Department said.

Ms. Geoghegan also said that over the last five years, her office rewrote pay packages so that they are primarily stock-based and limited executive perks and fringe benefits.

She also said Ally’s CEO hasn’t received a raise since he joined the company in late 2009, and average cash compensation for the top 25 executives is 4 percent below median cash salaries for executives at similar companies.

Both Ally and GM shareholders also have overwhelmingly approved the compensation packages for the companies’ executives in the past few years, suggesting they are comfortable with the levels.

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