Hagel, on a two-day visit to Japan as part of a tour of Asia, said Russia's annexation of Crimea had sparked worries among allies in the Pacific and elsewhere.
Japan is locked in a bitter dispute with China over islands in the East China Sea, and some analysts have warned that Russia's move in Ukraine could embolden Beijing or other powers to take unilateral action to settle territorial claims.
Although his trip was planned long before Russia's incursion, Hagel said "another reason I'm here is to reassure our allies of our commitments to their security".
He said US defence ties with Tokyo had strengthened in recent years with the deployment of advanced surveillance aircraft to the country and plans to station a second early-warning radar there later this year.
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"I don't think there's any indication or any evidence that we're doing anything but strengthening our commitment to the security of Japan," he said.
Washington has warned China against trying to resolve the disagreement through force.
The crisis over Ukraine came up at a gathering of ASEAN defence ministers hosted by Hagel earlier this week in Hawaii, a defence official said.
But the topic was raised only "tangentially" and "there wasn't a lot of hand wringing over Ukraine and what will happen in their part of the world," the official, who spoke on condition of anonymity.
The Philippines and some other Southeast Asian states have accused China of aggressively asserting its claims and Hagel - without openly referring to Beijing - said there was no place for "bullying."
"You always have concerns when these issues continue to play out and drag out. And you always have concerns when there's any indication of coercion, intimidation, or bullying," he told reporters travelling on his plane.