"The coordinates of all of these targets were given to us by opposition representatives," senior military official Andrei Kartapolov said, without specifying which groups Moscow had cooperated with.
Kartapolov said Moscow's jets hit targets close to Palmyra, Deir Ezzor, Ithriya and eastern Aleppo with assistance from the opposition, destroying "terrorist" command posts, munition stores and anti-aircraft artillery.
Moscow has been bombing targets in Syria since September 30, when it launched an offensive in support of forces loyal to President Bashar al-Assad against Islamic State jihadists and other "terrorist" groups.
"Our aim both in Syria and anywhere else is to fight terrorism first of all," Putin said in Moscow on Tuesday.
Signup to our newsletter and follow us on Facebook and Twitter!
But the US and its allies, who are involved in a separate air campaign against IS, have accused Moscow of primarily hitting more moderate groups fighting Assad's regime.
Moscow said it had set up "working coordination groups" aimed at bolstering the fight against the IS, but said the identities of those involved were being kept secret.
"Such close cooperation will allow us to unite the efforts of the government troops with other patriotic forces in Syria that used to be in the opposition and act as a united front against the common enemy -- international terrorism," the defence ministry said in a statement.
Deputy foreign minister Mikhail Bogdanov said the contact with the opposition groups was "useful", both in terms of "fighting terrorism and promoting the political process," speaking to Interfax news agency.
The defence ministry said Tuesday that since the start of the operation it had hit 2,084 targets in 1,631 sorties, including 52 training camps and 287 command posts.
It said it has managed to cause "significant losses to the terrorists" and to "undermine their morale."