"At the moment, unfortunately, our partners are not ready to work within the format of single coalition," Putin's spokesman Dmitry Peskov told reporters.
He added however that Russia remained open to cooperation "in any format our partners would be ready for."
After jihadists killed 130 people in Paris this month in attacks claimed by IS, Hollande travelled to Moscow on Thursday, hoping to bolster global efforts to crush IS.
Putin had urged global powers to band together in the fight against jihadists in September during an address to the United Nations General Assembly, just before Russia launched its own bombing campaign in Syria.
Separately, a US-led coalition that includes France had already been staging air strikes against IS targets in Syria for over a year.
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Putin and Hollande agreed Thursday to coordinate strikes and share intelligence in what was the most concrete sign of progress from the French leader's diplomatic marathon that has also included talks with the leaders of the United States, Germany, Britain and Italy.
But the idea of a single anti-IS coalition involving Western powers and Russia did not get off the ground as US President Barack Obama is said to have given a cool response to Hollande's proposal.
The downing of a Russian warplane by NATO member Turkey in Syria has also cast a shadow on the diplomatic efforts to step up the fight against the jihadists.
While Turkey said Friday it wanted to calm tensions with Russia and local media said Ankara "temporarily" suspended air strikes against IS targets in Syria, the Kremlin said Russia would press ahead with its bombing campaign in the war-torn country.
"We proceed from the fact that the Russian air force is continuing an operation to support an offensive by the Syrian armed forces against terrorist organisations," Peskov said.
He added that Putin discussed the crisis with his aides at a meeting of his national security council on Friday.
"The meeting discussed increased tensions over Syria against the background of Turkey's aggressive and unpredictable actions," Peskov told reporters.