Outside the club, young people hugged, looking shocked as they waited for information after the fire that broke out in the early hours in Atalayas, on the outskirts of the city.
"I think we left 30 seconds to one minute before the alarms went off and all the lights went out (and) the screams saying there was a fire," one survivor, who was not identified, said.
"Five family members and two friends are missing."
Diego Seral, of Spain's National Police, told reporters the dead were found in the Fonda nightclub, one of three adjoining clubs, which had sustained the majority of fire damage, including the collapse of its roof, he added.
The collapse was making it difficult to locate victims, and it was difficult to pinpoint yet where exactly the fire started, he said.
The identification of the bodies would take time, he said. The emergency services gave the death toll, which has risen steadily throughout the day, as 13. The cause of the blaze is being investigated.
Earlier, Murcia's Mayor Jose Ballesta told reporters seven bodies had been found in the same area of the first floor, where the fire broke out.
A spokesperson for the Teatre nightclub, Maria Dolores Albellan, told reporters the fire originated in the neighbouring club, La Fonda, before spreading to the two adjoining clubs.
Spanish media reported several birthday celebrations were taking place at the time.
Ballesta declared three days of mourning for those who had died. Flags were lowered to half mast outside Murcia's City Hall.
Footage released by Murcia's fire service showed firefighters working to control flames inside the nightclub. The fire had destroyed part of the roof, the footage showed.
"We are devastated," Ballesta said on Spanish TV channel 24h, adding rescuers were still searching for several people reported missing.
Ballesta told 24h the fire started at around 6am local time and had now been brought under control.
Four people have been treated in hospital for smoke inhalation.
