Five years into the development of its Automated Commercial Environment (ACE) -- Customs' new multiyear, multibillion-dollar import and export processing system -- the agency still faces management challenges and risks associated with its development, the GAO said.

And although the U.S. Department of Homeland Security, which oversees Customs, has made progress implementing previous GAO recommendations, progress on the ACE management has been slow, the report said.

"For example, DHS has more to do to implement the recommendation that it establish an ACE accountability framework that, among other things, ensures that expenditure plans report progress against commitments made in prior plans," the report says. "Implementing a performance and accountability framework is important for ensuring that promised capabilities and benefits are delivered on time and within budget. In addition, describing progress against past commitments is essential to permit meaningful congressional oversight."

One of the problems Customs has run into is its pattern of borrowing resources from future releases of the system to address problems with the quality of earlier releases. This kind of activity has led to cost overruns and schedule delays, the GAO said.

"This pattern has continued with the most recently deployed cargo release, which developed problems that caused delays with a subsequent screening and targeting release," according to the report.