Residents in the area reached by telephone said security forces withdrew at dawn from the King Faisal neighbourhood after cutting off all roads leading to the mosque. No further details were immediately available.
Saudi security officials were not available for comment and the official Saudi Press News Agency said it had received no statement yet from the interior ministry regarding the incident.
Earlier the Al-Jazirah daily reported on its website that security forces surrounded the Suhail bin Saad mosque where a wanted suspect was believed to have taken refuge following a car chase.
The Al-Jazirah daily on Thursday reported on its website that security forces had encircled the mosque at 10:00 pm (1900 GMT) on Wednesday in the King Faisal neighbourhood east of Riyadh.
A witness told Al-Jazirah that a wanted suspect had taken refuge inside the mosque following a chase with security forces.
Security men disabled the vehicle in which the two suspects were riding. They managed to apprehend one of them while the other fled to the mosque.
The paper said there were conflicting eyewitness accounts as to whether there was an exchange of gunfire between the suspects and the security forces.
It added that there was heavy security presence in the area and that all roads leading to the mosque had been cut off and that mosque remained surrounded as of 4:00 am (0100 GMT) on Thursday.
Saudi Arabia is fighting an internal battle against what it calls "terrorists" and frequently announces the capture of suspects or weapons.
The last such announcement came one week ago when authorities said they arrested seven suspects and large amounts of arms and explosives during a raid in Riyadh after six security men were killed while searching another suspect's home.
Last year two car bombs on residential compounds in the capital in May and November killed 52 people.