Firefighters were battling a blaze that broke out at one of the facilities of the Rotem Amfert chemicals factory near Dimona on Wednesday.
Factory emergency services, who were helping to fight the fire along with 17 firefighting crews, said that there was not known to be anybody trapped in the facility.
The firefighters were all evacuated from the facility, which was in danger of collapsing. Biohazard teams were also on the scene.
One firefighter fell sustaining light injuries while fighting the blaze and an employee took ill from breathing in noxious fumes. Fire crews were fighting to prevent the blaze from spreading to the factory's ammonia production facility.
Rotem Amfert is a subsidiary of Israel Chemicals which produces complex fertilizers and phosphate fertilizers.