It is difficult to predict when or where tornadoes might occur, the IPMA added.
The storm hit the area around 11:00 GMT on Saturday and lasted until 15:00, it said.
Among the 28 injured across both sites in Albufeira there are six children, aged between two months and seven years, who were all lightly injured, and 23 adults, aged between 24 and 70, Portugal’s National Medical Emergency Institute said.
Faro, Setúbal and Beja – also in southern Portugal – remain under an orange warning for persistent rain today, sometimes heavy and accompanied by thunderstorms, according to the IPMA website.
On Friday, the Faro area was affected by very intense and localised gusts of wind, bringing down trees.