Google Inc. founders Larry Page and Sergey Brin may have to dig deeper to operate their fleet of private jets, after the U.S. Department of Defense ended a little-known arrangement that for years allowed the tech billionaires to travel on sharply discounted jet fuel bought from the Pentagon.

The agreement between the Google founders and the government, which started in 2007, ended Aug. 31 after officials at the National Aeronautics and Space Administration—which sponsored the arrangement—opted not to renew it, according...