A government watchdog has detected key deficiencies in the Federal Deposit Insurance Corp.’s internal controls that led to errors in the agency’s 2009 draft financial statements for its deposit insurance fund.

The errors, which involve the FDIC’s estimates of the loss-share transactions it has used to resolve bank failures, have been corrected. Under a loss-share transaction, a healthy bank agrees to acquire essentially all the assets and deposits of a failed bank and the FDIC agrees to share in the losses on the pool of assets.

The agency didn’t  catch errors totaling $386 million in its estimates of loss-share transactions, the Government Accountability Office said in a report released Monday.

The errors were spread over 25 percent of the total 93 individual loss-share estimates for 2009.

The GAO said the errors didn’t prevent the FDIC from accurately reporting its financial results for 2008 and 2009, but they  caused concern about the FDIC’s internal controls.

“Despite the large percentage of estimates with errors and the relatively high dollar impact of these errors, they were not detected by FDIC in the normal course of preparing the initial estimates, when updating the amounts for year-end reporting, or in its process for preparing and reviewing the DIF’s 2009 financial statements,” the GAO wrote in its report.

The FDIC, in a letter to the GAO, acknowledged the control weaknesses and said it was working to remedy them.

“The FDIC believes that additional resources added throughout 2009, control improvements implemented during the fourth quarter of 2009 and control enhancements to be completed by the end of the second quarter of 2010 will largely address the GAO’s concerns in this area,” FDIC Chief Financial Officer Steven O. App wrote to the GAO.

The FDIC has increasingly relied on loss-sharing arrangements to protect its insurance fund amid a surge in bank failures.

Forty-one banks went bust in the first quarter of this year, costing the fund an estimated $6.3 billion. The FDIC is working to rebuild its insurance fund, which went negative last fall.