Many more commercial airline flights take off every day than there are federal air marshals to fly with them. So the Federal Air Marshal Service has to make hard decisions about how best to deploy those undercover agents in the sky.

A recent report by a federal watchdog agency suggests that the marshals and the Transportation Security Administration, which oversees the program, should use more hard data in its risk-assessment process and better document its deployment decisions as well. That would lead to greater transparency and accountability to make sure they’re using their resources wisely, according to a report issued last month by the Government Accountability Office.

The air marshals’ complex scheduling process tries to balance the marshals’ assignments between domestic and international flights, while also deploying the agents according to the relative risk posed by different geographic areas within the United States. Right now, although risk data is factored in, those determinations are largely based on assessments that draw on the experience and expertise of officials in the agency, the GAO says. The watchdog report suggests, however, that federal air marshals shift from decisions by seasoned professionals to more data- and intelligence-driven analysis.

“We want to make sure that these air marshals are on the right flights,” GAO spokeswoman Jennifer Grover said Wednesday. “A well-documented and well-grounded risk assessment process would be a good way to validate the decisions that have been made.”

A TSA spokesman said Thursday the agency and the marshals agree with the GAO findings on better integrating risk-based factors in deployments and have already implemented two of GAO’s recommendations. The agency is working on implementing the others, the spokesman said in an email.

The report comes as the TSA has been struggling to meet two sometimes conflicting mandates: screen passengers closely to ensure their safety without causing undue delays at checkpoints. Recent history — including long lines at airports and several reports by oversight agencies — have suggested that the beleaguered agency was doing neither to anyone’s satisfaction. And more passengers than ever are flying.

The Federal Air Marshal Service, which has been around since the early 1960s to combat hijackers, ballooned in size following the Sept. 11, 2001 terrorist attacks. The agency went from having 33 air marshals to thousands, while its budget rose to as high as $906 million in fiscal 2012. In fiscal 2015, its budget was $790 million. The agents are assigned to ride on U.S. airliners in the United States or on international flights to countries with agreements in place to handle them. They are not deployed aboard foreign-flagged carriers.

Of 238 flights deemed to have the highest risk from 2010 to 2014, there were 150 with air marshals aboard, for a coverage rate of 63 percent, the GAO report says*. (The TSA calculated the rate differently, according to a more complicated scoring system that takes into account its performance targets across a range of risk levels, the GAO says.)

–This post has been updated and corrected to reflect that the numbers used by the GAO in its report are not actual numbers, which a TSA spokeswoman said were deemed too sensitive for release in a public document. She said the GAO supplied hypothetical numbers to illustrate its methodology of calculating coverage.