Royal Media said the CAK switched off its ADN signals at the Limuru station, disabling all transmission. Radio stations in parts of the country have also been affected.
Nation Media's free to air platforms are also down because of control by the authority but access through DSTV has not been interrupted.
Wachira Waruru, who is Royal Media Services managing editor, confirmed the shutdown and said they were looking into solutions.
"We would like to confirm that this morning the Communication Authority disconnected Citizen and Inooro TV transmission," he said.
"There has been no official communication as to why this action was taken. We are actively engaging the relevant government authorities to establish the reason for this action."
Waruru said they hope to resume normal transmission as soon as possible.
The authority is yet to give a comprehensive report on the shutdown but on Monday, the government threatened to switch off and revoke the licenses of media houses that cover the controversial swearing-in of the two Opposition leader.
According to Ipsos, Royal Media and Nation are the most influential brands, respectively, in Kenya.
RMS beats Nation Media Group, the region’s biggest media house, which runs Nation, Kenya’s leading newspaper in terms of circulation and readership.
NMG also runs NTV and two radio stations. Standard comes in at position three.
Kenya Editors Guild chairman, Linus Kaikai, took issue with the summoning of media managers from the main media houses to State House, where shutdown threats were reportedly issued.
Editors were divided after allegations that State House on Friday threatened to shut down TV stations that will broadcast the event live.
Kaikai said the direct threat was subsequently echoed off record by other senior members of the government.
-Nancy Agutu