At a meeting in Kazakhstan, Putin and the leaders of ex-Soviet states agreed to create a joint task force to defend the region's borders in the event of a crisis.
The deal could pave the way for the deployment of Russian and other troops along unstable Tajikistan's 1300-kilometre (808-mile) frontier with Afghanistan.
Read: Russia will not conduct ground operation in Syria: Putin
"The situation there (in Afghanistan) is genuinely close to critical," Putin told the summit of the Commonwealth of Independent States (CIS).
"Terrorists of different stripes are gaining more influence and do not hide their plans for further expansion," he said in Burabay, a popular tourist destination around 250 kilometres north of the capital Astana.
"One of their aims is to break into the Central Asian region," Putin said of the radical groups.
"It is important for us to be ready to react in concert to this scenario."
US President Barack Obama on Thursday said American troops would remain in Afghanistan past 2016, retreating from a major campaign pledge as he admitted Afghan forces were not ready to stand alone against the resurgent Taliban.
Read: When Obama and Putin crossed swords at the UN
Russia has military bases in the ex-Soviet nations of Kyrgyzstan and Tajikistan and -- with local militaries ill-equipped -- many in the region look to Moscow to shore up the region's vulnerable southern frontier with Afghanistan.
Tajikistan's porous border with the conflict-torn country is of particular concern given the surge in fighting between the Afghan government and the Taliban.
Instability in Afghanistan's north, highlighted by the Taliban's brief capture of the strategic city of Kunduz last month, has spurred talk that Russian troops could step in to secure the border.
Tajik political analyst Abdugani Mamadazimov, however, said that it is unlikely that the Kremlin will take over guarding the frontiers.
"For Russia to have a base in the country is one thing. But the border is a matter of national sovereignty for the Tajik government," he told AFP.
Read: Putin, at UN, calls for broad coalition against IS
While Russia is warily eyeing the upsurge in fighting in Afghanistan, its main focus remains on Syria, where it is carrying out a bombing campaign to support Syrian President Bashar al-Assad.
Putin praised the more than two-week-old air campaign, saying that Russia's strikes had "destroyed dozens of command posts, munitions depots, hundreds of terrorists and a large amount of military hardware".
Russia, he insisted, was only targeting "terrorists" in Syria and there was "a time limit" on the air campaign linked to a ground offensive by Assad's forces.
He added that "according to various estimates" there were between 5,000 to 7,000 people from Russia and the former Soviet countries of the CIS fighting with IS.
The US and its allies in a coalition targeting Islamic State jihadists have slammed Moscow's intervention in Syria and say Russia is hitting moderate groups battling Assad.
Putin has dismissed the criticism and accused Washington of refusing to coordinate with Russia over the bombing campaign.
On Friday, he sounded a more conciliatory tone, saying Russia was in a "negotiation process" with regional powers including Saudi Arabia and the United Arab Emirates and "was making attempts to build cooperation with the United States and Turkey".
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