"You've seen a range of troops massing along that border under the guise of military exercises," he said in a television interview in Vatican City. "But these are not what Russia would normally be doing."
Mr Obama said the moves might be no more than an effort to intimidate Ukraine, but could be a precursor to other actions.
"It may be that they've got additional plans," he said.
Mr Obama made his comments at the end of a visit to Europe, where the US, Germany, France, Britain, Italy, Japan, and Canada warned Russia it faced additional damaging sanctions if it takes further action to destabilise Ukraine.
Governments in Washington and Europe are in talks about measures against Russia's energy sector but have said they would hold off on more sanctions unless Moscow goes beyond the seizure of Crimea.
Mr Obama lamented that Russian President Vladimir Putin seemed stuck in a Cold War mentality.
"You would have thought that after a couple of decades that there'd be an awareness on the part of any Russian leader that the path forward is not to revert back to the kinds of practices that you know, were so prevalent during the Cold War," he said.
Russia's defence minister told Mr that all Ukrainian servicemen loyal to Kiev had left Crimea and the Russian flag was flying over all military sites.
Warships, war planes and other military hardware seized by Moscow will be returned to the Ukrainian army, Defence Minister Sergei Shoigu told Mr Putin.
"The recent events in Crimea were a serious test," Mr Putin was quoted by Russian news agencies as saying. "They demonstrated both the completely new capabilities of our Armed Forces and the high morale of the personnel."
Russian forces took control of Crimea ahead of a referendum there this month in which residents voted overwhelmingly in favour of the region becoming part of Russia.
Russia's foreign ministry has claimed that ethnic minorities in Ukraine are living in fear after the removal of the country's president and the coming to power of interim authorities that include right-wing nationalists, Russia's foreign ministry has claimed.
The statement by the ministry was in line with Russia's frequent contention that Ukraine's large ethnic Russian community faces repression under the new government that Moscow characterises as fascist.