"We have prevented IS fighters from re-establishing a command post in the Hama province that had been destroyed," spokesman Igor Konashenkov said.
The ministry said an IS training camp and command post in northwest Idlib province were also hit.
Putin rejected allegations that civilians had been killed in Russian raids, dubbing the reports "information warfare".
The air strikes came as Russia presented a draft resolution to the UN Security Council that would call for consent from Damascus for attacks against the Islamic State group in Syria.
Washington had previously blocked a similar resolution, and no date has been set for a vote on this one.
The Syrian conflict, which began as protests against Assad's regime in 2011, has escalated into a multi-faceted war that has drawn thousands of jihadists from overseas.
Moscow, a key Assad ally, had earlier said its raids destroyed a "terrorist" headquarters, a weapons warehouse, a command centre and a car bomb factory.
But a Syrian security source said the strikes targeted Islamist rebels, the Army of Conquest, which includes Al-Qaeda's Syria affiliate the Al-Nusra Front and which fiercely opposes IS.
- 'Target IS' says Hollande -
Hollande said, ahead of his talks with Putin, that air strikes in Syria should target IS, not other groups.
He said it was essential to ensure that "the strikes, regardless of who is carrying them out, target Daesh and not other groups".
Turkish Foreign Minister Feridun Sinirlioglu said he felt "serious concern over the information that Russia's air strikes targeted opposition positions instead of Daesh".
Sinirlioglu was to meet US Secretary of State John Kerry later Friday.
Russian Foreign Minister Sergei Lavrov has rejected the accusations, saying Moscow saw "eye-to-eye" with the US on striking IS and Al-Nusra.
"If it acts like a terrorist, if it walks like a terrorist, if it fights like a terrorist, it's a terrorist, right?" he asked.
Asked if it was true that Russia and the United States were on the same page, Kerry said: "Well, in concept, but we are not yet where we need to be."
US Senator John McCain accused Russian warplanes of striking groups "funded and trained by our CIA," saying Moscow's real priority was "to prop up Assad".
And one US-backed rebel group, Suqur al-Jabal (Falcons of the Mountain), said Russian warplanes attacked its training camp in Idlib province.
The group has received training and equipment as part of a $500-million US programme to build an anti-IS force.
A US-led coalition has carried out near-daily strikes on IS in Syria for more than a year, saying it had "not altered operations in Syria to accommodate new players on the battlefield".
Pentagon spokesman Colonel Steve Warren told reporters coalition planes had conducted sorties and air strikes in Syria over the past 24 hours.
After complaints by the US that Russia gave just an hour's notice of Wednesday's attacks, the two sides held so-called de-confliction talks by teleconference, US officials said.
"We made crystal clear that at a minimum the priority here should be the safe operation of the aircrews over Syria," Pentagon press secretary Peter Cook said.
- 'Coordinating with Damascus' -
After weeks of Russian military build-up in Syria, Russian senators on Wednesday unanimously approved armed intervention.
It remains unclear how much of the opposition fighting Assad's army -- including the Western-backed opposition -- is considered by Moscow as a potential target.
Kremlin spokesman Dmitry Peskov appeared to acknowledge that Russia was targeting not only IS, saying it operates according to a list apparently agreed with Damascus.
"These organisations are known," he was quoted as saying by Russian news agencies. "The targets are determined in coordination with the Syrian defence ministry."
A Russian foreign ministry official said Moscow could broaden its campaign to Iraq if Baghdad asks, but Lavrov later told reporters Moscow was "not planning to expand our air strikes to Iraq".
Russia's defence ministry said Moscow had sent more than 50 military aircraft as well as marines, paratroopers and special forces into Syria.
Russia and the West are in deep disagreement over Syria, with Western powers blaming Assad for starting a war that has left more than 240,000 people dead and millions displaced.
Moscow portrays Assad as the only force stopping the spread of IS and argues he must be part of the conflict's political solution.