At least six people were killed and more than 3,000 evacuated after two days of severe rain in southeastern Spain.

A man who had been missing since leaving his home on foot earlier on Friday was found dead in the village of Redovan in Valencia. Another was found in Granada province after his car was swept off a motorway and a third man in Almeria after trying to drive through a flooded tunnel, rescue services said.

Two people died on Thursday when floodwaters caused by torrential rain dragged their car and flipped it over in eastern Spain, local emergency services said.

The victims, siblings aged 51 and 61, were killed in the region of Castilla La Mancha, a spokesman for the government delegation in the region said.

A total of 74 roads were closed, as was the entire Murcia regional railway service, and the Murcia airport. The railway link between Alicante and Spain's two main cities - Madrid and Barcelona - was shut, acting Interior Minister Fernando Grande Marlaska said, calling the floods "a serious tragedy".

Some affected areas saw record daily rainfall for the month of September and remained flooded throughout Friday.

"The situation is critical, all the municipality is full of water," Mario Cervera, mayor of the town of Alcazares, one of the most affected in Murcia, told Spain's state-run TVE channel.

Rescue workers, including over 1,500 army troops, were using helicopters and boats in various areas.

"This man was holding onto a traffic sign. ... The officer and I jumped to take him out," one emergency worker told Reuters.

In addition to some 1,500 people evacuated earlier, another 2,000 residents of the town of Santomera in Murcia were removed from their homes pre-emptively due to a controlled release from a local dam to avoid its overflowing, the interior minister said.

"The forecasts are now more positive than around midday. We have reports that point to diminishing dangers and risks of further flooding," he told reporters while visiting the affected areas, warning though that residents and authorities had to remain cautious.

Authorities have recommended citizens stay at home in the affected areas and avoid using their cars.

Tourists were left stranded in Alicante airport as many flights were delayed or cancelled.

"We've been in the queue here four or five hours, it's very difficult to get to the toilet, impossible to get anything to eat," Haydn Harding, a 78-year old diabetic tourist from Northern Ireland, said at the airport.

Acting Spanish Prime-Minister, Pedro Sanchez also visited Orihuela on Saturday, one of the worst effected cities. He expressed the government's solidarity and support. He said that no material resource or human effort would be spared in the effort to assist those affected by the flooding.