Prime Minister Benjamin Netanyahu issued the order after talks with health and airport officials on Thursday evening.
His spokesman Mark Regev told AFP that the move was to be implemented immediately.
An exercise was being held at Ben Gurion International Airport, the main international entry point to Israel, in which the arrival of a passenger with Ebola was to be simulated.
“The exercise will include initial questioning as well as evacuation and hospital treatment,” a government statement said.
Ebola has killed around 4,500 people this year, nearly all of them in the West African countries of Liberia, Guinea and Sierra Leone, according to the World Health Organisation (WHO).
There have been no reported cases of Ebola in Israel or the Palestinian territories.
Israel is a popular destination for African Christian pilgrims. Around 43,000 of them have visited the country since the start of the year, according to the tourism ministry.