Prime Minister António Costa said the measure will apply from midnight on April 9 until midnight on April 13.
The national airports will be closed in an "exceptional measure that aims to prevent circulation from abroad to Portugal or from Portugal to abroad".
He clarified that there are established exceptions such as cargo flights, of a humanitarian, state, military nature and those necessary for the repatriation of Portuguese abroad.
The closure is likely to affect Ryanair passengers, with flights from the UK to Lisbon being one of the few routes still in operation.
Portugal's flag carrier TAP has already grounded thousands of flights, and is temporarily laying off around 90 per cent of staff.
The only remaining routes are for medical cargo, repatriation, or flights to the island of Madeira and the Azores.
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The government has also banned "any travel outside the municipality of habitual residence, except for people who have to travel to exercise professional activities" during the Easter period.
At a press conference to announce the latest measures, he said: "The effort we have made, which has resulted from exemplary behaviour, has produced good results.
"The pace of growth in new cases has slowed, but more effort needs to be made and intensified over these five days to accelerate the pandemic control process."
He said the five day travel ban would "be decisive" when a decision is eventually taken to lessen the restriction orders.
The government has also renewed the state of emergency for another 15 days.
The prime minister explained: "If decreeing a state of emergency was necessary 15 days ago, it is essential that we renew it today.
"All the effort we have made so far will be compromised if it does not continue."
After Easter, airports will reopen but flights will only be allowed to transport one third of their passenger capacity.
Health authorities expect the outbreak to plateau at the end of May, after reporting the first death on March 16.
A 14-year-old boy from Portugal is one of the youngest victims of coronavirus in Europe.
Teenager Vitor Godinho tragically died in a hospital near Porto in the early hours of Sunday morning after falling ill with the virus.
The schoolboy suffered from psoriasis, a skin disorder that affect the immune system.
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