Top diplomat for East Asia, Kurt Campbell, said those ties have grown in recent years, but not fast enough.
Campbell was speaking Tuesday at a gathering of the U.S.-Indonesia Society in Washington.
The U.S. severed military ties for several years after of Indonesia's bloody crackdown in East Timor in 1999. Jakarta has since sought to professionalize and modernize its military. Key U.S. restrictions on engagement with Indonesia's feared special forces were lifted in 2010.
Human rights groups say Indonesia's military abuse continues, particularly in the restive province of west Papua.
Campbell also advocated deeper ties between the two governments and praised Jakarta's leadership in regional diplomacy.