The explosion occurred at about 2:15pm on Monday at a fireworks factory near Pinseque.
Spain's Civil Guard confirmed that a body had been found in the early hours of Tuesday morning, bringing the number of dead to six. Another six people - three woman and three men between the ages of 25 and 57 - were seriously injured in the explosion.
The cause of the explosion is still not known.
Varios desaparecidos y al menos tres heridos tras la explosión de una pirotecnia en Zaragoza http://t.co/L7jhqMZYCu— noticiaseconomicas (@nociticaseconom) August 31, 2015
Those injured have been transferred to a nearby hospital for treatment.
Ha explotado una fábrica de pirotecnia en Zaragoza, varios heridos y desaparecidos. pic.twitter.com/1Yet5mxFjy— KAJAL (@kajalnapalm) August 31, 2015
The sound of the explosion could be heard fup to 20 kms away and neighbours reported feeling the ground shake, according to EFE.
Spanish television images showed plumes of smoke rose from warehouses at the factory.
Spanish Prime Minister Mariano Rajoy, who is currently meeting with Angela Merkel in Germany, tweeted his condolences: "From Germany, I would like to send my condolences to the families to those who died in Zaragoza, and I hope that the injured get well soon":
Desde Alemania, quiero hacer llegar mi pésame a las familias de los fallecidos de #Zaragoza y mis deseos de recuperación a los heridos. MR— Mariano Rajoy Brey (@marianorajoy) September 1, 2015
The same fireworks company also suffered an accident in 1984 when several explosions destroyed seven warehouses where fireworks were stored, according to El Pais.
The Pirotecnia Zaragozana factory employs around 40 people.
August is a busy time for fireworks factories in Spain as many small towns celebrate religious festivals at this time of year with fireworks shows.