Pyongyang has threatened to hit the US Pacific territory with "enveloping fire," sparking dire warnings from US President Donald Trump.
Itsunori Onodera told reporters that Friday's missile, which overflew Japanese territory, flew 3,700 kilometres - "long enough to cover Guam", which is 3,400 kilometres (2,100 miles) from North Korea.
"We cannot assume North Korea's intention, but given what it has said, I think it has Guam in mind," Onodera said.
He warned that "similar actions (by the North) would continue" as Pyongyang appeared to have shrugged off UN sanctions agreed earlier this week.
But, for the second time in less than a month, it overflew Japan's northernmost island of Hokkaido, sparking loudspeaker alerts and warnings to citizens to take cover.
Japanese Prime Minister Shinzo Abe said Tokyo could "never tolerate" what he called a "dangerous provocative action that threatens world peace".