The ban, which affects passengers from Sierra Leone, Guinea and Liberia, will be effective from Tuesday midnight, Xinhua quoted health cabinet secretary James Macharia as saying in a conference in Nairobi.
"This step is in line with the recognition of the extraordinary measures urgently required to contain the Ebola in West Africa."
"This decision has been arrived at after extensive consultations with key stakeholders," he said. The suspension also applies to all Kenya ports of entry.
"The ban will exclude health professionals supporting efforts to contain the outbreak as well as Kenya citizens returning home from the three countries," Macharia said.
He added these passengers will have to undergo extensive screening and thereafter close monitoring and where necessary shall be quarantined.
According to the health cabinet secretary, all five suspected cases of Ebola in Kenya have tested negative for the virus.
The World Health Organisation (WHO) has declared the Ebola outbreak in four West African countries a public health emergency.
Over 2,000 suspected cases of Ebola have been reported in West African countries and half of them were killed since earlier this year, the WHO said.
Kenya Airways later issued a statement confirming that it will suspend commercial flight operations to Liberia and Sierra Leone temporarily.
However, the statement said it will continue operating all its scheduled flights to Nigeria and Ghana, but it reserved the right to cancel flights depending on the situation.
The ban affects passengers from Sierra Leone, Guinea and Liberia
"To our esteemed guests who are booked on the suspended flights, we wish to express our sincere regrets for disrupting your travel plans. We further wish to confirm that we shall be providing for a full refund of all tickets earlier booked and paid for prior to this suspension," it said.
Kenya Airways is a leading African airline flying to over 60 destinations worldwide, 40 of which are in Africa and carries over three million passengers annually.