The government has directed the Inspector General of Police Hillary Mutyambai to designate holding places for those who violate the curfew order.
Health Chief Administrative Secretary Rashid Aman made the revelation while speaking at Afya House on Sunday.
"We are aware Kenyans are keeping away from utilizing health facilities for fear of contracting the disease. We assure that precautionary measures have been taken by hospitals. Curfew breakers will no longer be accommodated at the usual government quarantine facilities," he said.
On Friday, the government disclosed that some 1,254 Kenyans have been arrested in 38 counties over the violation of the nationwide curfew imposed by the government in a bid to restrict the spread of the Covid-19 pandemic in the country.
Interior CAS Hussein Dado said those arrested include 1,198 civilians, 38 police officers and 10 Kenya Defence Forces soldiers.
Others arrested during the period also include four prison warders, four National Government Administration Officers, three judicial officers and a National Intelligence Service (NIS) officer.
Dado said Officers Commanding Police Stations are under instructions to present suspects before court within 24 hours following their arrests.
"Curfew violators fall in the category of petty offenders. Since violators are arrested during the hours of the night, the suspects are taken to the police station and presented in court the following day to be dealt with according to the law," the CAS said.
He added that officers on duty had been advised to observe guidelines for the prevention of Covid-19 in the interaction with suspects and water and soap have been installed at the stations for washing of hands.
Those arrested are also expected to be put under mandatory quarantine for 14 days at their own cost.
President Uhuru Kenyatta last week extended the dusk to dawn curfew and cessation of movements into and of Nairobi, Mombasa, Kilifi and Kwale counties for a further 21 days after first imposing it on March 26.
The head of state said that the measures have helped the country avoid the projected number of infections where it had earlier been estimated that by the end of April there would be close to 10,000 coronavirus cases in the country.
He warned that if the trend continues, more stringent measures will be effected in the mentioned counties.