The fatalities comprised the pilot and all three passengers -- a Swiss and three French nationals -- who were aboard the aircraft, plus a Portuguese truck driver 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 about a kilometre from an aerodrome at Tires, in the district of Cascais about 20 kilometres from central Lisbon.
The dead comprised the pilot, who was French according to Portuguese media, three passengers and the truck driver.
Two of the French victims were Marseille surgeon Jean-Pierre Franceschi, 65, and his wife Nathalie, Marseille mayor Jean-Claude Gaudin said in a statement late on Monday.
Gaudin expressed his condolences to their families and paid tribute to the "internationally recognised orthopaedic surgeon (....) a leading authority in the sports world".
A knee specialist, Franceschi had notably operated on legendary former France striker Jean-Pierre Papin, the 1991 Ballon d'Or winner, and former France and Arsenal star Robert Pires.
According to a statement issued by the aerodrome, the plane belonged to Symbios Orthopaedics, a company based near Lausanne, Switzerland that specialises in orthopaedic prosthetics.
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.
About 90 firefighters mobilised to fight a blaze, which was quickly put out. A neighbouring house was also damaged.