Brigadier Mansur al-Turki told journalists early on Wednesday that his troops had laid siege to a house in the al-Qasim region, 370km north of the capital Riyadh.
He said that security forces were "facing heavy fire from [people hiding] inside the house."
Witnesses said a shootout started around 10:45pm (1945 GMT) local time on Tuesday as security forces raided a house in the Ashrafya quarter in Unaiza.
Although al-Turki could not provide information about casualties "until the picture becomes clearer", other security sources suggested that two security officers had been wounded.
Saudi Arabia is fighting a fierce battle against various factions seeking major political change in the oil-rich desert kingdom.
Some 90 people have died and hundreds more wounded since May 2003.