Six people are still missing in Greece two days after a flash flood killed 16 people near the capital. Picture: Xinhua/Lefteris Partsalis

Athens - Six people are still missing in Greece two days after a flash flood killed 16 people near the capital, the fire department said Friday.

"We are looking for two additional people whose disappearance was declared to police," a fire department spokesperson said.

"That brings the total to six," he said.

The Greek government on Wednesday declared a three-day state of mourning after the freak flood struck the towns of Mandra, Nea Peramos and Megara, some 50 kilometres (30 miles) west of Athens.

Some elderly people died inside or near their homes, drivers were trapped in their cars as they drove to work, and two bodies were found at sea.

"We have never seen such a storm. Five months of rain fell in just a few hours," Megara mayor Grigoris Stamoulis told state TV ERT.

One of the missing is apparently a hunter. The other was last seen at a roadside canteen, the spokesperson said. Several people were trapped there when the flood struck.

At the height of the disaster, the deluge exceeded three metres (10 feet) in some areas, witnesses said. Three highways were flooded, submerging and carrying away even trailer trucks.

Over a hundred firefighters were in the area for a third day, clearing debris and racing against the clock to find people who could still be trapped under the mud.

"We are continuing to drain water (from properties) and to look for the missing, which is our priority," said fire department chief Constantinos Giovas.

Prime Minister Alexis Tsipras said he felt "shock" after touring the area Thursday.

"This is clearly a rare and extreme weather phenomenon," Tsipras said in a statement.

"But this extreme phenomenon had these effects because of (decades of) accumulated problems and deficiencies in infrastructure and zone planning," he said.

Experts have said ill-conceived building in the area -- some of it by local municipal authorities -- meant this was a disaster waiting to happen. 

Corrective drainage works for the area were approved in 2016 but work has yet to begin.

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

Late on Thursday, the capital was lashed by another thunderstorm and firefighters in northern Greece said they were called to drain water from over 400 homes. 

In the northern region of Pieria, nearly 40 people had to be rescued by firefighters, authorities said.