The accident occurred after a crane on the Saipem 7000 pipelay vessel suffered a mechanical failure, Medgaz said in a statement.
Spanish uni0n officials told news agency Efe a pipe fell on the workers as it was being positioned ahead of being pipelaying.
Three of the workers were crushed and three others were injured, emergency services officials said.
Accident: on board the Saipem 7000
A reuters report said all but one of the workers affected were employed by the Italian oil services group Saipem.
Spanish emergency services personnel, including a coast guard helicopter, reportedly had to obtain permission from Algerian officials before responding to the accident because the Saipem 7000 is currently operating in Algerian waters.
The injured were airlifted to the southern Spanish city of Almeria while the coast guard sent a helicopter to the vessel to search for the missing worker.
The 198-metre Saipem 7000 arrived in Almeria on 11 August to begin laying the 120-kilometre pipeline.
The Medgaz subsea gas pipeline will link Beni Saf, on the Algerian coast, with southern Spain, and is scheduled to be completed by next year.
Medgaz is a consortium of Algerian state company Sonatrach, Spanish groups Cepsa, Iberdrola and Endesa and France's GDF Suez.
Officials from the Medgaz consortium and Saipem were not immediately available for comment when contacted by UpstreamOnline.