In earlier raids on Saturday police detained three suspects and seized guns, grenades and "extremist literature", an Interior Ministry spokeswoman said.
In late January police stormed another apartment block in Nalchik and killed seven suspected militants inside. Russia's campaign against Islamic militants has intensified since the Beslan school siege in September, in which more than 330 hostages died, many of them children. Local officials in Nalchik say they have a list of 500 suspected rebels.
Nalchik lies in the foothills of Mount Elbrus and the rugged terrain provides a wealth of hiding places within a few hours' drive from Chechnya, where Russian troops have been fighting rebels for a decade. Fugitive separatist head Aslan Maskhadov has announced a month-long cease-fire from the start of February to mark his willingness to enter peace talks.