USDA and CBP spent $861 million checking travellers and cargo for farm pests in 2011, but fees left a $325 million gap because federal law limits who pays

The United States has long used border inspections to protect farms, forests and livestock from foreign pests and diseases. Every year, agricultural inspectors examine international passengers, vehicles, and cargo to prevent potentially destructive organisms from entering the country. But the system is expensive, and federal law limits how much of that cost the government can recover through inspection fees.

According to a March 2013 report by the US Government Accountability Office (GAO), the country spent $861 million on its Agricultural Quarantine Inspection (AQI) programme in the 2011 financial year, while the fees collected fell more than $325 million short of the total cost. The programme was jointly administered by the US Department of Agriculture’s Animal and Plant Health Inspection Service (APHIS) and the Department of Homeland Security’s Customs and Border Protection (CBP). The funding gap highlighted a central problem: the agencies had to protect American agriculture but could not charge every category of user for the inspections they received.

Why inspection fees fell short


The main aim of the AQI program was to screen out invasive insects, plant pests and animal pathogens before they could threaten American agriculture. The screening process covered passengers arriving from other countries, commercial flights and ships, trucks and rail freight, and incoming cargo shipments. However, the process relied, to some extent, on the fees paid by certain groups of people and firms.

The GAO found that APHIS did not have enough authority to recoup inspection costs through user fees. Travellers and transporters of certain types were excluded from payment, and there were occasions when not all the costs incurred in providing inspection were accounted for by the agencies. Some payments were also not collected due to administrative problems. This created a large gap between programme costs and fee revenues. Public funding had to cover the shortfall, even though the inspection system was partly designed to recover its own costs. The GAO recommended improvements to fee calculation and collection, while Congress considered expanding fee-charging authority.

A funding imbalance between two agencies

The problem was also worsened by the way inspection costs and fees were split between the two departments. CBP shouldered well over 80% of the overall cost of the program in 2011, although it got only 60% of the fees collected from such inspections. On the other hand, APHIS accounted for 19% of the total cost of the program but received 36% of the fees generated by it. In other words, CBP had to rely on congressional funding to operate.

The consequences went beyond government accounting. Agricultural pests can damage crops, threaten livestock and impose substantial costs on farmers and consumers. A study published in Science of the Total Environment documented the considerable economic burden associated with biological invasions in the United States, reinforcing the importance of preventing harmful species from entering the country. That meant balancing efficient border control with a fair system for paying the costs. Raising fees could recover more of the program’s costs, but the government could not charge everyone involved without legal authority.

Reforms sought to close the gap.

The GAO called on the USDA and the Department of Homeland Security to calculate fees more accurately, improve collection, and distribute revenues more fairly. At the same time, it recommended that Congress expand the power of the USDA to collect all expenses connected to agricultural inspections. Several steps were taken to address some of these issues. APHIS introduced more categories of fees, such as one paid by cruise passengers, while CBP improved its procedure for identifying unpaid fees for some commercial vehicles and vessels.

In 2024, APHIS updated its regulation concerning agricultural quarantine and inspection fees; some amendments were implemented in October 2024, and others would be implemented in April 2025. Nevertheless, these measures did not necessarily solve all the structural problems brought up by GAO. The main problem was that the government lacked authority to charge the full cost of a program that benefited the entire economy, not just the people paying the fees.