FSB officers seized 6.5 kg (14.3 lbs) of Afghan heroin hidden in the gasoline tank of a vehicle driven by a Kazakh national, who was arrested when he entered the city.
"A 22-year-old Kazakh national was detained yesterday carrying high-quality Afghan heroin from Kazakhstan to Russia," the domestic security service said. "The drugs were planned to be sold in [Russia's] Federal Siberian District."
The heroin was in 12 packages stamped with known 'trademarks' of Afghan drug barons - "999," "888," and "Scorpio" - the service said.
The suspect faces a prison term of seven to 20 years, if found guilty.
Former Soviet republics in Central Asia are major transit countries for drugs from Afghanistan, the world's largest heroin producer.
Another 5 kg of heroin (11 lbs) and 15 kg (33 lbs) of cannabis were seized from a suspected member of a Russian criminal group in a separate FSB operation also conducted on Thursday.
"A 43-year-old Russian, ethnic Ingush, bought 5 kg of heroin and 15 kg of cannabis in Novosibirsk. The batch was to be sold in the [neighboring] Kemerovo Region, where he came from," the FSB said.
The suspected drug dealer also faces up to 20 years in prison.