The regional president of eastern Valencia, Carlos Mazon, said it was still too early to give an exact death toll, with many people still missing.
Mr Mazon spoke after Spain’s national broadcaster RTVE reported that 13 bodies had been found in Valencia, citing the Civil Guard.
The Civil Guard did not immediately return calls from The Associated Press.
Rainstorms on Tuesday caused flooding across a wide swath of southern and eastern Spain.
A high-speed train with nearly 300 people on board derailed near Malaga, although railway authorities said no one was injured.
High-speed trains between Valencia and Madrid were disrupted, as were several city lines.
The storms are forecast to last until Thursday, according to Spain’s national weather service.