The European maritime security agency detected what it believed was pollution in the sea around 80 kilometres south of Faro on Tuesday.
However, an investigation by an aircraft found it to be layers of water of different temperatures.
Commander Marques Ferreira said: “It is not pollution. Layers of water of different temperatures were detected which give the sea various colour tones.
“It is a good sign that we have powerful means with which to monitor our waters.”