Greek Prime Minister Alexis Tsipras on Wednesday declared a state of mourning after a freak overnight downpour with the force of a "waterfall" flooded three towns near Athens, killing at least 15 people.

"At this time, declaring a state of national mourning over this great tragedy is the least we can do," Tsipras said in a televised address.

"I pledge that we will stand next to the families of the victims with all the means at our disposal," he added.

The flooding, described as the worst in 20 years, early on Wednesday struck the towns of Mandra, Nea Peramos and Megara, a semi-rural area west of Athens where many factories and warehouses are based.

"The water came down the mountain, millions of tonnes," Nea Peramos deputy mayor Stavros Fotiou told state broadcaster ERT as locals braced for another night of heavy rainfall.

"Our roads are completely destroyed... 1,000 homes have been flooded, that's a third of the town," he added.

The greater Athens governor's office said the "force and danger posed by the (weather front) is unprecedented."

"We had another incident in 1999 but it was nothing like this," said Megara mayor Grigoris Stamoulis.

Television images showed tanker trucks, buses and lorries nearly completely submerged in the reddish mud torrent snaking through entire neighbourhoods.

Over a dozen people were hospitalised, state agency ANA said. One person was missing.

The fire service reported 13 dead and the coastguard two more.

The dead, men and women aged 35 to over 90, included a handful of people who perished inside or near their homes, a truck driver, a hunter, and two men who were carried by the raging water miles (kilometres) out to sea.

More than a dozen people were rescued from an intercity bus, while others fled a Johnson & Johnson factory whose outer wall collapsed.

The prime minister's office said 87 people had been rescued overall.

Tsipras said the army would help house the homeless.

Greece's civil protection authority said three highways had been severed with traffic rerouted.

- 'Niagara Falls' -

"The situation is very difficult, the Niagara Falls came down and could not be stopped," deputy regional governor Yiannis Vassileiou told ERT.

"The weather forecast is poor, so we are on alert," he said.

"A river of debris went through Mandra... This is unprecedented," Vassileiou said.

"Everything is lost, the disaster is biblical," Mandra mayor Ioanna Kriekouki told the station.

"We have people who are trapped... we need machinery to get them out of their homes," said Kriekouki, who was also immobilised in her home.

Parts of the area were without electricity and authorities said many people would need shelter for the night while the deputy mayor of the town of Nea Peramos, which was without water, said repairs may take up to five days.

"Access to the area is difficult, debris has nearly reached the height of homes," said fire department spokesman Yiannis Kapakis.

The deputy governor said rubble-clearing equipment had been moved to the area but could not be used until the water levels subside.

Prime Minister Alexis Tsipras said the deaths had been caused by a "disastrous flood" and expressed deep sorrow for the deaths.

The fire service said it had received more than 600 calls for help and dispatched nearly 200 firemen to the area.

A prosecutor ordered an investigation into building violations in the area.

Geologist Dimitris Papanikolaou said ill-conceived construction in the area meant this was a disaster waiting to happen.

"We chose this very area as a test case for flooding," Papanikolaou, a professor at Athens university, told ANA radio.

"(It's) a mountainous area with a network of small rivers coming together in a torrent that had been blocked for over 500 metres...there was nowhere for the water to go," he said.

Two people had died in flooding in the area in 1996, Papanikolaou noted.

Stricken areas will request EU solidarity funds, the governor's office said.

On Tuesday, intense rain had also struck the eastern Aegean island of Symi, without causing victims.

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