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The system also gives Customs officers tools to identify and stop potentially dangerous or illegal imports.
UPS said the system had enabled it to save about $70m (£45m) by eliminating the need for a separate Customs Service building to be added to its facilities.
According to US law, imported goods are required to be handled separately from domestic shipments. However, with UPS's tracking and sorting systems, which are very tightly controlled, both can be loaded into the general sorting operation.
Tracking labels on the packages allow selected shipments to be routed automatically to US Customs inspectors for a closer look.
Previously, inspectors had to manually scan long import reports, looking for clues that would lead them to suspect packages.
If an inspector spotted a package that seemed too large for its declared contents or a shipment from a country known as a drug haven he would have the package X-rayed, sniffed by a dog or searched.
But with the volume of packages increasing - WorldPort has a sorting capacity of 304,000 packages an hour - Customs needed to find a faster, more efficient way to get the job done.
UPS said its software allows US Customs inspectors to filter through shipping manifests using any search query they choose, including the name of the shipper or recipient, the description of the goods or the weight or declared value of a shipment.
Inspectors can also set up recurring filters that constantly scan for patterns that identify packages requiring further inspection.
The automated sorting system also gives inspectors more control over package flow, reducing the chance that a targeted package is released before clearance.