"We can confirm that some bodies have already been found," Carlos Mazon told reporters, without saying how many.
Authorities could not give further details until relatives had been informed, he added.
Heavy rain lashed much of eastern and southern Spain on Tuesday, flooding streets with muddy water and disrupting rail and air travel.
Images shot by residents with smartphones and broadcast on Spanish TV showed raging waters washing away cars and flooding buildings.
In some areas, more than a month's rain fell in a single day, Spanish media reported.
"We are facing an unprecedented situation, which nobody remembers," Mazon said.
Officials said on Tuesday that at least seven people were missing -- a truck driver in the Valencia region and six people in the town of Letur in the eastern province of Albacete.
Emergency services workers backed by drones would work through the night to look for the missing in Letur, the central government's representative in Castilla-La Mancha, Milagros Tolon, told Spanish public television station TVE.
"The priority is to find these people," she added.
- Crisis committee -
Spain central government set up a crisis committee which met for the first time late Tuesday to overlook the response to the storm.
"I am closely following with concern the reports on missing persons and the damage caused by the storm in recent hours," Prime Minister Pedro Sanchez wrote on X, urging people to follow the advice of the authorities.
The government has deployed the UME, a military unit specialised in rescue operations, to Valencia to help local emergency services.
Valencia city hall said all school classes and sports events were suspended on Wednesday, and parks would remain closed.
Twelve flights that were due to land at Valencia airport were diverted to other cities in Spain due to the heavy rain and strong winds, Spanish airport operator Aena said.
Another 10 flights that were due to depart or arrive at the airport were cancelled.
National rail infrastructure operator ADIF said it had suspended all rail services in the Valencia region "until the situation returns to normal for the safety of passengers".
High-speed trains between Madrid and the city of Valencia will be suspended until "at least" 10 am on Wednesday due to the effects of the storm, it added.
A high-speed train with 276 passengers derailed in the southern region of Andalusia, although no one was injured, the regional government said in a statement.
Emergency services used helicopters to lift people from homes and cars in Alora in Andalusia after a river overflowed.
State weather agency AEMET declared a red alert in the Valencia region and the second-highest level of alert in parts of Andalusia. Several roads were cut in both regions due to flooding.
Meteorologists said the storm was caused by cold air moving over the warm waters of the Mediterranean Sea, which produced intense rain clouds.
The rains are expected to continue until at least Thursday.
Scientists warn that extreme weather such as heatwaves and storms is becoming more intense as a result of climate change.
Flood strands 600 in French holiday village
Marseille (AFP) Oct 28, 2024 -
Almost 600 people were trapped in southern France Monday after flooding damaged the bridge on the only road to a holiday village, with a local mayor saying authorities were working to evacuate them.
"The sun is shining today and there's water, electricity, nobody's panicking," said Liliane Boyer, mayor of Le Muy -- around halfway between Marseille and Nice in southeast France.
"All the authorities are working to allow the holidaymakers who were supposed to depart today or this week to leave," she added.
France is in the middle of a two-week autumn school holiday when many families vacation elsewhere in the country.
The Canebieres holiday village of houses and trailers was hosting 584 people when intense rain and flooding hit France's southeast over the weekend.
Three people were evacuated by helicopter for health reasons late Sunday and taken to hospitals in the region, the Var department prefecture said.
Others needing to leave have to ask to be ferried out of the village in all-terrain vehicles along forest tracks before travelling onward by train or plane, the Canebieres village said on its website.
But they will have to return later to pick up their stranded cars, it added.
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