Speaking at a convention of the International Association of Campus Law Enforcement Administrators in Hartford, Mueller said the ruling "does throw a lot of things up in the air."
By a 5-4 vote last week, the nation's highest court struck down the District of Columbia's 32-year-old ban on handguns, the first major pronouncement on gun rights in history. It upheld the right for communities to license guns.
Mueller said communities will have to determine their own license programs. As a former Marine who served in Vietnam, he said "I tend to believe weapons harm people and more often than not they harm the people carrying them."
With his grandchildren going to college, Mueller said he hopes "those campuses will be weapons free."
Mueller said the FBI's top priority remains counterterrorism, counter-intelligence and protecting the secrets of the United States.
He said college campuses and small communities could be "potential incubators of terrorism" even while major cities such as New York and Los Angeles remain primary targets for terrorists.
"The fact is we can't rule out any community in the United States as a potential incubator of terrorism," Mueller said.