"According to our intelligence, the number of [Daesh] members alone in northern Afghanistan is about 2,000 people," the Russian president said during a video conference meeting with leaders of other ex-Soviet states, AFP reported.
Putin earlier this week warned of the threat of veteran militants from Iraq and Syria with Daesh links crossing into Afghanistan, while Russia's Foreign Ministry said it expected the Taliban, which recently gained control of the country, to deal with the threat.
On Friday, he said Daesh leaders in Afghanistan are seeking to project the terror group's influence across former Soviet states in Central Asia – which Moscow sees as its backyard – to stir up religious and ethnic discord.
"Terrorists are seeking to infiltrate the Commonwealth's territory, including under the guise of refugees," Putin said, referring to a group of ex-Soviet countries – some of which border Afghanistan in Central Asia.
The Taliban, which seized control of Kabul from a pro-Western government in mid-August, are seeking international recognition, as well as assistance to avoid a humanitarian disaster.
Putin's special envoy to Afghanistan, Zamir Kabulov, told Russian news agency Interfax Friday that Taliban representatives would attend an international conference in Moscow next week alongside regional players Iran, China and Pakistan.
Putin on Friday said there was no need to rush with official recognition of the Taliban but noted that "we understand that we need to interact with them".
In the 1980s, Moscow fought a disastrous decade-long war in Afghanistan that killed up to two million Afghans, forced seven million more from their homes and led to the deaths of more than 14,000 Soviet troops.