Immigrations and Custom Enforcement cannot account for all visa overstays due to inefficiencies in the agency, according to a new report.

ICE arrested just 0.4 percent of visa overstays it could account for, according to an audit by the inspector general.

The agency has 27 different databases used to investigate and track immigrants who remain in the country past the deadline issued on their temporary visas. The lack of a cohesive system has "produced numerous inefficiencies," making ICE ineffective at catching visa overstays who may pose security risks, according to the audit.

"Department of Homeland Security IT systems did not effectively support ICE visa tracking operations," the inspector general said. "ICE personnel responsible for investigating in-country visa overstays pieced together information from dozens of systems and databases, some of which were not integrated and did not electronically share information. Despite previous efforts to improve information sharing, the DHS Chief Information Officer (CIO) did not provide the oversight and centralized management needed to address these issues."

The inspector general said ICE agents are not receiving proper training to use the systems, which can contain up to 40 different passwords for ICE officers to login.

"Because of these systems and management limitations, DHS could not account for all visa overstays in data it annually reported to Congress," the inspector general said.

"Manual checking across multiple systems used for visa tracking contributed to backlogs in casework and delays in investigating suspects who potentially posed public safety or homeland security risks," the inspector general added.

ICE reported to Congress there were 527,127 nonimmigrant overstays in 2015, but the numbers did not include student visas or anyone who crossed the border from Mexico or Canada.

"Because of unreliable collection of departure data at these ports of entry, the Department could not account for these potential overstays," the inspector general said. "Therefore, the report was limited in that it only included individuals traveling to the United States by air or sea on business travel or tourism."

Of the more than 500,000 identified overstays, only 3,402 were arrested, which amounts to less than 0.4 percent.

ICE's databases also had inaccurate information recorded on those who were arrested.

"In some cases, the individuals arrested had been reported in DHS systems as having already left the United States," the inspector general said. "Because this information was not recorded, ICE personnel were unable to provide an exact number when asked during our audit."

The United States issued more than 10.8 million nonimmigrant visas in 2015. The inspector general said that although only a small percentage overstay their visas, those individuals could pose severe national security risks.

"For example, two of the 19 hijackers on September 11, 2001, were visa overstays," the inspector general said. "This prompted the 9/11 Commission to call for the government to ensure that all visitors to the United States are tracked on entry and exit."

The audit noted that the department has 27 different databases for handling visa overstays, leading ICE officers to be "unsure of which system to use." There are 17 separate systems that are used only for conducting the initial part of the overstay investigation.

Even the most experienced officers have trouble navigating the ICE database system. One agent with over two decades of experience said he was not aware of a database that is often used for national security vetting of overstays.