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The fatalities comprised the pilot and all three passengers -- a Swiss and three French nationals -- who were aboard the aircraft, plus a man who was at the warehouse at the time, they said in a statement.
Three other people were slightly injured.
The warehouse, operated by the Lidl supermarket chain, is located about a kilometre (half a mile) from an aerodrome at Tires, in the district of Cascais about 20 kilometres (12 miles) from central Lisbon.
The twin-engine Piper PA-31 plane had just taken off on a flight to the southern French city of Marseille when it crashed, hitting a truck parked at the warehouse.
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About 90 firefighters mobilised to fight a blaze, which was quickly put out. A neighbouring house was also damaged.
The aerodrome issued a statement saying that the plane belonged to Symbios Orthopaedics, a company based near Lausanne, Switzerland that specialises in orthopaedic prosthetics.