In unusually forceful remarks, Mr Hagel also said China must show more respect to its neighbours.
The defence secretary drew a direct line between Russia's takeover of Ukraine's Crimea region and the ongoing territorial disputes between China, Japan and others over remote islands in the East China Sea.
"I think we're seeing some clear evidence of a lack of respect and intimidation and coercion in Europe today with what the Russians have done with Ukraine," Mr Hagel told reporters after a meeting with Japanese defence minister Itsunori Onodera in Tokyo.
"We must be very careful and we must be very clear, all nations of the world, that in the 21st century this will not stand.
"You cannot go around the world and redefine boundaries and violate territorial integrity and sovereignty of nations by force, coercion and intimidation, whether it's in small islands in the Pacific or large nations in Europe."
Mr Hagel travels to China later this week to discuss regional tensions, and said the Asian nation was a "great power".
He added: "With this power comes new and wider responsibilities as to how you use that power, how you employ that military power. All people deserve respect, no matter how large or small."