Police on Thursday surrounded a house in a district north of Riyadh and exchanged fire with several wanted armed men inside, killing two, a security source said.
The gunfight lasted four hours starting 6:00 am (0300 GMT).
Saudi Interior Ministry spokesman General Mansur al-Turki confirmed a security operation was taking place in the area.
"The police are trying to apprehend one or more individuals who are putting up some resistance," he said, but did not give further details.
Dubai-based Al-Arabiya satellite television had initially said four suspects were killed in the exchange of fire.
It later reported the death toll was two, saying another one rebel had been wounded while another was captured.
The shoot-out was the first since
King Abdullah assumed power
An interior ministry spokesman said "no security force members were wounded".
Clashes also erupted between police and suspects in the
southwestern holy city of Medina, with security forces detaining an unspecified number of people, the satellite channel said without identifying those held.
Authorities have killed or captured all but three men on a list of 26 most wanted suspects published in 2003. In June, officials listed another 36 wanted men they are hunting. It was not clear if the men shot on Thursday were on the lists.
The shoot-out was the first such incident since the new King Abdullah came to the throne in the oil-rich Gulf kingdom, and follows a spate of warnings from Western embassies about possible terror attacks.
Wave of violence
Saudi Arabia, the world's top oil exporter, has been battling a wave of violence by al-Qaida linked rebels over the past two years, much of it against Western targets.
Earlier this month, the US embassy in Saudi Arabia temporarily closed while Britain, Australia and Canada have since also warned that terror attacks may be imminent.
King Abdullah succeeded his late half-brother king Fahd on 1 August, but had been de facto ruler of the ultra-conservative kingdom for about a decade.