Weapons of mass destruction and "potential instruments of terrorism" could be at risk of entering the country through cargo rail shipments, according to a new watchdog report. 

The scathing inspector general investigation claims Customs and Border Protection agents working at ports of entry aren't properly screening rail cargo coming in from Mexico and Canada. In turn, CBP cannot say for sure whether they made the right move in releasing various "high-risk" shipments into the U.S. 

CBP policy requires port inspectors to use "large-scale non-intrusive inspection equipment" to scan shipments that its automated system flags as high risk. This process is supposed to let inspectors screen cargo for everything from drugs to weapons to other contraband. 

The policy also requires that ports use radiation detection equipment when inspecting high-risk rail shipments.

The audit, however, revealed CBP agents, who operate within the Department of Homeland Security, failed to consistently do both on rail shipments entering the United States from Mexico and Canada.

Officers “may have failed to require examinations of rail shipments that were at higher risk to contain contraband, dangerous goods or weapons of mass destruction,” the report concluded. “CBP may also have failed to detect potential instruments of terrorism or dangerous materials from entering the United States.”

The IG report based its findings from a sample of 254 high-risk rail shipments from six ports that processed much of the overall fiscal 2012-2013 shipments. The report found that officers used incorrect targeting data criteria on 23 percent of the shipments tested.

The report also found officers did not always use the required radiation detection equipment to examine the shipments, missing the mark 72 percent of the time in the IG test.

Another glaring problem is that CBP officers did not record the results of their rail shipment checks properly. One reason is that some of the officers were not trained to use the tracking system called CERTS.

Using CERTS at rail ports in the country was mandated on April 13, 2011. The report said inspectors found evidence that at some sites, employees conducted physical exams on the cargo but failed to document the findings.

Government investigators made six recommendations to DHS to fix the problems, which include making sure officers are using the mandatory targeting system for "scoring" rail shipments, reiterating to supervisors their responsibility to make sure officers document their finds accurately and providing additional training on using the automated targeting system.

The agency said it would fix the problems highlighted in the inspector general report and work to update its guidance and patch up agent training gaps.

Additionally, the department says it’s drafting “a current comprehensive National Cargo Targeting Policy that will develop system enhancements to CERTS that will enable CERTS to generate reports to identify high risk shipments not in compliance with policy.”

The department estimates the new policy will be completed by June 30 of this year.