The SNB said in a statement it had information showing that Islamic militants with alleged ties with Al-Qaeda were plotting armed attacks and sabotage operations in a number of places, including the city of Osh.
The claim came amid widespread domestic and international criticism at Kyrgyzstan's recent moves against alleged militants.
On August 6, Kyrgyz law enforcement agencies killed a prominent ethnic Uzbek imam during a security raid in Osh. The SNB initially said Rafiq Qori Kamoluddin was an IMU militant, before suggesting he may have been killed accidentally.
On August 9, Kyrgyzstan deported to Uzbekistan four UN refugees and one asylum seekers wanted in their home country for allegedly taking part in the May 2005 unrest in Andijon.
International organizations have criticized the move, saying it violates the 1951 UN convention on refugees.
Kyrgyz opposition leaders and rights campaigners have accused the government of imitating Uzbekistan's heavy-handed tactics against religious dissent.
The also blame authorities for allegedly collaborating closely with the Uzbek security services.
Kyrgyz officals have denied the accusations, calling them unfounded.