People quarantined at Pride Inn Lantana hotel in Nairobi and all other private facilities will have to foot their bills.
The government says anyone who chose to enter into a private arrangement with hotel facilities will have to meet their obligations because they had a choice of staying in government facilities.
"Individuals who chose government-owned quarantine facilities were moved to such facilities," government Spokesman Cyrus Oguna said in a statement Saturday following uproar from the individuals that the government had declined to pay for their accommodation.
The individuals have been staying at the hotel after a mandatory 14-day quarantine to confirm their COVID-19 status.
The initial agreement was for them to stay at the facility for two weeks, but the government added 14 more days, after some people turned positive, for what Oguna said was failure to observe the social distancing regulation.
"The additional quarantine period was necessary to protect the rest of the society from the disease," he said.
There are hundreds of Kenyans in quarantine while the number of confirmed cases stood at 191 by Saturday. Seven people have succumbed to the virus while 24 have recovered and discharged from hospital.