The authority said historically vulnerable areas - such as Lisbon, Faro and Albufeira - could flood again because of the amount of rain expected.
In the warning issued on its website today (Friday, 6 May), the ANPC warned the population that rainfall of between 10 and 20 millimeters an hour could be expected in certain parts of the country, at times accompanied by thunder, over Saturday and Sunday.
Some places such as southern Portugal can expect up to 50mm of rain in 12 hours, during the course of Saturday night and the early hours of Sunday, it continued.
Strong gusts of wind of up to 100km/h can also be expected in high-lying locations.
A set of recommendations on how to best protect against the impending stormy weather has also been issued.
Thursday the Algarve city of Faro flooded in the areas of São Luís, Conceição and Faro, following rain which fell non-stop in the region for most of the day.
Information from Faro Council states 35 people called the emergency services for help with flooding in homes, shops and warehouses and well as in public places like car parks and theatres.
For more see: www.ipma.pt or: www.prociv.pt
I observed today that most of the drainage ditches alongside the hilly bits of the Avenida dos Descobrimentos in Albufeira are still blocked with clay, rocks and other debris. So any excess water will flow down the road and into the town instead of into the drains.
Why is not anyone's responsibility to clear these ditches? It wouldn't take long.
By Thomas Allen from Algarve on 06 May 2016, 17:45