The government will screen travellers entering the country through the JKIA, Busia and Malaba border points following an Ebola outbreak in DR Congo, that has killed 17 people.
Health CS Sicily Kariuki on Wednesday said the move is aimed preventing Kenyans from being infected with the deadly virus.
The move comes after the Congolese government made the declaration on May 8.
Local health officials reported 21 patients showing signs of hemorrhagic fever around the village of Ikoko Impenge, near the town of Bikoro before the outbreak was confirmed. Seventeen later died.
"We have installed Thermal Guns to detect any person with elevated temperatures. Further to this, we have established the National Health Emergencies Council whose role among others will be to act expeditiously to prevent any importation of Ebola or any other disease of public health importance," the CS said.
The virus is transmitted to people from wild animals and later to human beings through human to human transmission.
A statement from the DRC's health ministry said that medical teams the World Health Organisation and Medecins Sans Frontieres were dispatched to the zone on Saturday and took five samples from suspected active cases.
Two of those samples tested positive for the Zaire strain of the Ebola virus.
This is the ninth time the country has reported an Ebola outbreak.
"Our country is facing another epidemic of the Ebola virus, which constitutes an international public health emergency." the country's health minister said in a statement on Tuesday.
Kenya issued an Ebola alert in May last year following a similar outbreak in the DRC.
The ministry re-activated rapid response teams and follow up cases of travellers with elevated body temperature, and asymptomatic cases who came into the country.
In case a person presents Ebola-like symptoms, an isolation ward was already set up at the Kenyatta and the Moi Teaching and Referral Hospital.