But he maintained Turkey had a right to defend its airspace and charged that Russian air activity near the Turkey-Syria border has been an "ongoing problem."
Turkey said Tuesday it shot down the Russian plane with a missile strike after repeated warnings to the plane that it had flown over its territory.
Saying he expected to speak with Turkish President Recep Tayyip ErdoÄŸan in the coming days to discuss the incident, Obama urged Russia and Turkey to communicate about the details of the operation in order to decrease the chance of escalation.
The downing of the Russian plane complicated Hollande's visit to the White House, where he pressed Obama for greater global cooperation on battling ISIS, including with Moscow.
Hollande has openly called for a greater international effort to push back ISIS, whose killing spree in Paris two weeks ago was the worst terror attack on French soil in more than half a century.
He said Tuesday greater cooperation between the United States and Russia is required in battling ISIS, though persistent U.S. skepticism about Putin's intentions in Syria have until now prevented any significant military coordination between the two countries.
"We want to gather all countries," Hollande said. "We do not want to exclude anyone."
But he also said Russia must pledge to target the Islamic State terrorists instead of moderate Syrian forces opposed to the government of Bashar al-Assad, a requirement Obama also insisted upon during Tuesday's press conference.
"The strikes against the moderate opposition only bolster the Assad regime," Obama said, noting that many of those opposition fighters have the support of Turkey and that the Russian strikes are taking place very close to the Turkish border.
Obama said that he and Hollande agreed that Russia could help in the fight against ISIS if it changed the focus of its military activities in Syria.
"Russia could play a more constructive role if it shifts the focus of its strikes to defeating ISIS," Obama said.
He also said the U.S. and France were sharing intelligence information to help France coordinate its strikes on ISIS and called on Europe to do more to stop the flow of foreign fighters, share passenger lists and exchange information across borders.
Obama also cited the incident with Turkey as a reason for Russia to turn its focus to fighting only ISIS in Syria, saying that "some of those conflicts or potential for escalation are less likely to occur" if it narrowed its sights.
He said the encounter also "underscores the importance of our moving the political track along as quickly as possible" when it comes to resolving the Syrian civil war, which ISIS has exploited to seize territory.