"We are disappointed," Putin's top foreign policy aide Yury Ushakov told reporters, adding it was clear to Moscow that the decision was linked to the fugitive US intelligence leaker Edward Snowden who was granted asylum in Russia last week.
"It is clear that the decision is linked to the situation over the employee of the American special services Snowden which was absolutely not created by us," he said.
Ushakov said the situation showed that the United States was still not ready for relations "on an equal basis" with Russia but said the invitation for Obama to visit still stood.
"We are ready to work further with the American partners on all key questions on the bilateral and multilateral agenda," he added.
Obama is still set to visit Russia for the G20 summit in Saint Petersburg but he had been scheduled to hold a meeting with Putin in Moscow ahead of that event.