The US and Russian military will hold talks "as soon as possible" to avoid clashing in Syria, the countries' top diplomats say.
But the US expressed fears the targets were non-IS opponents of Russia's ally, Syrian leader Bashar al-Assad.
The US is targeting IS with air strikes in both Syria and Iraq.
Nato said there had been little co-ordination by Russia with US-led forces against IS, also known as Isil. The US says it was informed of Wednesday's air strikes only an hour before they took place.
The New York Times and the Wall Street Journal report that US-backed rebels were targeted by Russia.
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Russia's Foreign Minister, Sergei Lavrov, said there was a need to "establish channels of communication to avoid any unintended incidents". His US counterpart, John Kerry, said talks will be held "as soon as possible," possibly as early as Thursday.
Mr Kerry added: "It's one thing to be targeting Isil, but the concern, obviously, is that this is not what was happening."
France's Defence Minister, Jean-Yves Le Drian, told French MPs: "Curiously, they didn't hit Islamic State. I will let you draw a certain number of conclusions yourselves."
Syria's civil war has raged for four years, with an array of armed groups fighting to overthrow the government.
The US and its allies have insisted that President Assad should leave office, while Russia has backed him remaining in power.
he Russian defence ministry said the country's air force had targeted IS military equipment, communication facilities, arms depots, ammunition and fuel supplies - and did not hit civilian infrastructure or areas nearby.
Syrian opposition activists said Russian warplanes hit towns including Zafaraneh, Rastan and Talbiseh, resulting in the deaths of at least 36 civilians, a number of them children.
None of the areas targeted was controlled by IS, activists said.
"We have been exposed to a wide range of weapons over the last five years," one doctor in Rastan told Reuters. "But what happened today was absolutely the most violent and ferocious, and the most comprehensive."
r Kerry said the United States would not object to Russian military action in Syria - as long as it was directed against IS and groups linked to al-Qaeda.
US Defence Secretary Ashton Carter went further, saying: "By supporting Assad and seemingly taking on everyone who is fighting Assad, you're taking on the whole rest of the country of Syria.
"At least some parts of the anti-Assad opposition belong in the political transition going forward. That's why the Russian approach is doomed to fail."
Analysis: Jonathan Marcus, defence and diplomatic correspondent
Russia's decision to intervene with its air power greatly complicates the Syrian crisis while probably offering little additional chance of a diplomatic resolution.There are serious questions about who exactly the Russian aircraft are targeting. US officials believe that the initial Russian strikes are not in IS-held territory, raising the possibility that Russian air power is being utilised more in the form of close air support for Syrian government forces against the multiple enemies of the Assad regime.
Of course, many of these enemies are supported by the West's Arab allies or Turkey. The warning time given by the Russians to the Americans announcing the start of their operations may also raise some eyebrows, suggesting that much more detailed co-ordination may be needed in future to avoid incidents in Syrian airspace.
In a televised address, Mr Putin said the air strikes were targeting Islamist militants - including Russian citizens - who have taken over large parts of Syria and Iraq.
"If they [militants] succeed in Syria, they will return to their home country, and they will come to Russia, too," he said.
He added that Russia would be "supporting the Syrian army purely in its legitimate fight with terrorist groups".
Mr Putin also said he expected President Assad to talk with the Syrian opposition about a political settlement, but clarified that he was referring to what he described as "healthy'' opposition groups.
Syria's civil war
What's the human cost?
More than 250,000 Syrians have been killed and a million injured in four-and-a-half years of armed conflict, which began with anti-government protests before escalating into a full-scale civil war.
And the survivors?
More than 11 million others have been forced from their homes, four million of them abroad, as forces loyal to President Assad and those opposed to his rule battle each other - as well as jihadist militants from IS and other groups. Growing numbers of refugees are going to Europe.
How has the world reacted?
Regional and world powers have also been drawn into the conflict. Iran and Russia, along with Lebanon's Hezbollah movement, are propping up the Alawite-led government. Turkey, Saudi Arabia and Qatar are backing the Sunni-dominated opposition, along with the US, UK and France.
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