The Internal Revenue Service is suffering from several new deficiencies in its internal controls, although it has managed to address a number of older problems, according to a new report from the Government Accountability Office.

The report comes in the midst of lingering questions over the IRS’s loss of two years of emails between the former director of its Exempt Organizations unit, Lois Lerner, and people outside the agency, after her computer crashed in 2011. The agency has been struggling with a series of budget cuts in recent years that have negatively affected taxpayer service.

During the GAO’s audit of the IRS’s fiscal year 2013 financial statements, it identified eight new internal control deficiencies. The GAO found, for example, that the IRS did not obtain sufficient, appropriate evidence to conclude whether internal control at service organizations that were responsible for operating information systems affecting the IRS’s financial reporting was effective as of Sept. 30, 2013. This item was also included in the GAO’s report on the results of its fiscal year 2013 financial statement audit as a contributing factor to the IRS’s continuing significant deficiency in internal control over financial reporting systems as of Sept. 30, 2013.

In addition, the GAO found that the IRS’s policies and procedures for time card approvals and follow-up of time card exceptions were not always effectively followed to reasonably assure that IRS employees’ time cards were proper and that staff did not receive excess pay.

The IRS also did not adequately monitor the receipt and acceptance transactions that its staff members entered into the agency’s procurement system, nor did it provide adequate staff training to reasonably assure the accurate and timely recording of goods and services received, the report noted.

There were also problems with the asset acquisition and disposal process at the agency. The GAO found that the IRS’s controls were not effectively designed and implemented to reasonably assure that the assets it acquired were accurately recorded in its asset management system on a timely basis, nor that adequate documentation and approval were obtained before assets were disposed, nor to assure that the assets disposed of by the IRS did not contain confidential taxpayer information or other sensitive information.

The IRS also did not have a formal process in place to estimate the financial statement impact of unrecorded installment agreement user fee revenue at year-end or criteria with which to measure the significance of this amount to objectively determine and document whether a year-end adjustment was necessary and, if so, to record an adjustment to reasonably assure that the user fees received were properly reflected in the IRS’s financial statements.

The GAO also found that the IRS’s controls were not effectively designed to prevent or identify—and resolve in a timely manner— duplicate installment agreement user fees charged to and collected from taxpayers.

The IRS also did not have sufficient controls in place to reasonably assure that refunds disbursed on behalf of deceased taxpayers were valid prior to disbursement.

In addition, the IRS’s controls were not operating effectively to reasonably assure that tax refunds were not disbursed to deceased taxpayers who did not have a personal representative or surviving spouse identified on their accounts to receive the refunds.

The IRS completed corrective actions on 26 of the 60 recommendations from the GAO’s prior financial audits and other financial management-related work that remained open at the beginning of the fiscal year 2013 financial audit. As a result, IRS currently has 51 recommendations that need to be addressed, consisting of the previous 34 open recommendations and the 17 new recommendations the GAO made in this latest report.

The report provides 17 recommendations to address the internal control issues the GAO has identified. The report also presents the status, as of Sept. 30, 2013, of IRS corrective actions taken to address 60 previous recommendations made by the GAO that remained open at the end of its fiscal year 2012 IRS financial statement audit.

The IRS agreed with all 17 of the GAO’s recommendations and described the actions the agency had taken, had under way, or planned to take to address the control deficiencies described in the report.

“We continue to make significant progress in addressing internal control deficiencies and financial management as evidenced by 14 consecutive years of clean audit opinions on our financial statements,” wrote IRS commissioner John Koskinen in response to the report. “During fiscal year 2013, IRS strengthened its processes and controls over the timely release of tax liens and transmittals of taxpayer receipts and information, as well as its oversight of duress alarms, allowing for the closure of several longstanding recommendations.”