GRU chief Lt. Gen. Igor Sergun said the situation in Afghanistan poses a "serious challenge to international stability" and that the withdrawal of the International Security Assistance Force (ISAF) in 2014 could increase the threat of terrorism and religious extremism.
"A diversified terrorist network, including suicide bomber training camps has already been established in the country and the Taliban has close links with foreign terrorist structures whose militants, having gained combat experience in Afghanistan, could be sent to other hot spots across the world," he said.
The situation could get even worse if those militants resume cooperation with Al Qaeda and use force to establish "a global caliphate" from Morocco to Malaysia, he said.
Nikolai Bordyuzha, general secretary of the Collective Security Treaty Organization, an intergovernmental military alliance headquartered in Moscow and consisting of former Soviet states, earlier warned that after the ISAF withdrawal from Afghanistan the situation in the part of the country near Russia's southern borders will worsen.
A zone of instability will emerge in regions bordering Afghanistan, and the influence of extremist groups will grow, as will the penetration of Islamist fundamentalist ideas in neighbouring states, Bordyuzha said.
Sergun also commented on the situation in war-torn Syria, saying that radical groups will continue to impose their conditions on the way the country is run, relying solely on the use of force.
That could provoke the country's breakup, an increasing flow of refugees to neighbouring countries and further destabilization of the situation, the GRU chief said.
He also pointed to the growing number of supporters of the armed jihad from Europe within the Syrian opposition.
"After they acquire practical combat experience they can be expected to return to their countries where they will be able to apply it on the European continent," he said.
Recently, Arab experts warned that Islamist forces coming to power in 'Arab Spring' countries could provoke a fresh wave of protests and lead to civil wars.
If Islamists come to power in Syria, it will divide the country, Basma Qodmani, a member of the opposition Syria National Council in 2011-12, said.
Ahmed Ezz El-Arab, deputy head of Egypt's Wafd Party, slammed the Islamists who have taken dominant positions in that country.
Muslim Brotherhood members who won the presidential election in Egypt "are using religion as a political tool, being patriots of their movement, not of Egypt", he said.
"Never has there been such an incompetent government in our country's history. They hijacked the revolution and now they want to bring in members of their movement in all positions of authority," he said.
"That will lead the country to a new revolution and a civil war."