Admiral Robert Papp, U.S. Coast Guard commandant, said that figure falls far short of President Barack Obama's goal of capturing 40 percent of drugs entering the country by 2015.
"Right now we're hovering probably closer to around 20 percent because of lack of resources out there," Papp told reporters.
The Coast Guard is charged with reducing the supply of drugs heading toward the United States through a 6 million square mile (15 million square km) area that includes the Caribbean, the Gulf of Mexico and eastern Pacific.
Papp said the Coast Guard is able to go after 39 percent of vessels it has identified as suspect that are moving between South America and Central America.
"So that means 61 percent just don't get addressed because of lack of resources," he said.
Papp said it was important to catch the large cocaine and marijuana shipments before they get to Central America, "where then these multi-ton loads are broken down into smaller loads and they come across the border in some way, shape or form."
To meet the automatic budget cuts known as sequestration, the Coast Guard reduced its operating budget by about 30 percent in 2013, the commandant said. That affected some missions more than others and drug interdiction was one of them, since the large ships burn expensive fuel, he added.
The agency seized 194,800 pounds (88,400 kg) of cocaine in fiscal year 2013, 41,000 pounds (18,600 kg) less than it did in 2012. Marijuana seizures dropped from 124,500 pounds (56,500 kg) in 2012 to 81,000 pounds (36,700 kg) in 2013, according to Coast Guard statistics.
The $300 million lost in sequestration, while not much by federal budget standards, was a big hit to the Coast Guard, Papp said. The agency has a number of mandatory programs, from regulating safety features on boats to intercepting people trying to enter the United States illegally. Its proposed budget for next year is $9.7 billion.
"For the Coast Guard, millions are still important," Papp said.