The extremist group still controls patches of territory in eastern Syria, where it imposes a media blackout.
"The mission of defeating the Islamic State bandit groups in Syria has been accomplished", Lt General Sergei Rudskoi, head of the general staff's main operations directorate, said as combat maps and footage of Russian planes and Syrian soldiers firing their guns in celebration flashed on the huge screen behind him at a security press briefing.
"Two hours ago, the (Russian) defense minister reported to me that the operations on the eastern and western banks of the Euphrates have been completed with the total rout of the terrorists", Putin said.
According to Rudskoy, the use of Russian warplanes, including strategic bombers, in the final stage of the Syrian liberation was "unprecedented". ISIL is an alternative abbreviation for the militant group.
"Of course there may still be isolated hotbeds of resistance", he said. Russian Federation had not previously acknowledged cooperating with the Kurds in the Syrian conflict.
But the Syrian Observatory for Human Rights, which monitors the conflict, said Thursday that IS still held about eight percent of the Deir Ezzor province. In recent weeks, the terrorist group has been progressively driven out of the country by a combination of Syrian government forces, Kurdish militias and Russia's Aerospace Forces.
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Russian Federation began its bombing raids in September 2015 in support of Syrian President Bashar al-Assad's beleaguered forces.
"But it is a big and prolonged task", he said.
Rudskoi said "separate sabotage bands of ISIL" could still be operating but would be fought by Syrian government troops, indicating that Russia's involvement would be scaled down. The intervention has helped forces loyal to Syrian President Bashar al-Assad, a close ally of Moscow, regain control over much of the country.
Putin had said in November that Russian Federation would start focusing on political reform as part of a "new stage" in the conflict.
The Syrian conflict began in 2011 and over 340,000 people have been killed.