Customs and Border Protection, the federal agency that monitors U.S. borders and international trade, is making cuts under budget sequestration that could lead to delays at ports.

In a letter to industry groups, Deputy CBP Commissioner David Aguilar said the staffing cutbacks could decrease service levels in port cargo operations.

With fewer people to inspect containers, there could be delays of up to five days or more at major seaports, and significant daily backups at land ports of entry, Aguilar said.

The major federal transportation programs, highway funding and safety, are mostly exempt from the sequester that went into effect March 1 because their money comes from the Highway Trust Fund. But other programs, such as CBP, are vulnerable to the cuts.

CBP is required to make significant cuts for the rest of this fiscal year, Aguilar said. The cuts include furloughs, reductions in overtime and a hiring freeze.

The agency will continue to make security its highest priority, and will continue to run such freight-related programs as the Customs-Trade Partnership Against Terrorism and the Free and Secure Trade program, he said.

But he said the agency expects significant potential impacts on cross-border travel and trade. Besides the container inspection slowdown, he warned of longer wait times at international airports and less flexibility on hours of operation generally.

“These cuts take place against a backdrop of significant growth of international travel and trade in all environments,” he wrote. International air travel is up 12% over the past three years and maritime and air cargo grew 4% last year, he said.

“CBP is very concerned about the ramifications of sequestration and we will endeavor to operate in a manner that is least disruptive to our mission and to your business.”