The system will be similar to the one introduced in the U.S. after the 2001 9/11 attacks.
Nikolai Patrushev also said a special crisis center would be set up within the Ministry of Foreign Affairs to protect Russian nationals and organizations abroad. Russia's government also approved a counter-terrorism program for 2009-2012 at the session.
"This year, the NCC will remain focused on reducing the terrorist threat," Patrushev said.
He also said Russia was taking steps to counter terrorist ideology and eliminate terrorist groups in the North Caucasus region.
The last major terrorist attack to take place in Russia was the September 2004 Beslan school siege, which left 333 people dead, including 186 children. The raid was carried out by forces loyal to the notorious Chechen militant Shamil Basayev, who was later killed by Russian troops in July 2006.
Patrushev said on Wednesday however that several terrorist attacks had been prevented during Russia's March 2 presidential elections. He did not give details.