"In the near future, we need to set up a unified system for detecting, preventing and defending against computer attacks on Russia's information (technology) resources," Putin said at a meeting of the FSB.
He added that the task should be completed as quickly as possible.
Last month, Putin issued a presidential order calling for such a system.
The move came a week after Kaspersky Lab, a Russian computer security company, announced it had detected highly sophisticated malware, dubbed "Red October", which targeted "diplomatic, governmental and scientific research institutions" in eastern Europe and former Soviet republics.
Kaspersky researchers said the majority of the affected computer systems were based in Russia and the virus had been created to "gather sensitive documents", including geopolitical intelligence, access to classified computer networks and personal data.
Addressing the FSB meeting, Putin said the main targets of spying are Russia's promising technologies and inventions, plans for development of the military forces and the defense industry, and crucial political and economic information.
"We need the most modern methods for organizing counter-espionage activity, including the protection of secret information," Putin said.
"This likewise concerns the increasingly frequent attempts to break into national electronic databases."
Putin also called for effective measures to counter attempts by radicals to use the Internet for their purposes.
"When neutralizing any kind of extremist structures, we should act as resolutely as possible, and block attempts by radicals to use information technologies, Internet resources and social networks for their propaganda," Putin said.
He said that effective counter-measures demand special operations that must be carefully planned but also entirely legal.
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