The weather agency said the very rare red warning of severe flooding and disruption covered Angus and southern Aberdeenshire and was in place for the whole of Saturday. It came as a second person was confirmed to have been killed after a falling tree hit a van near Forfar on Thursday evening.
More localised than the red warning in force for Friday morning, it centres on the town of Brechin, where hundreds of homes have been inundated by flood water, as well as the coastal town of Montrose.
Rescue services have had to extract residents by boat who had not evacuated after Thursday's order for about 350 homes in the town, after the river reached 4.4 metres and breached the town's flood barriers.
Meanwhile, in England, the Environment Agency issued further flood warnings covering 105 sites, largely clustered around Bristol, the Midlands and Yorkshire, with a string of warnings along the east coast stretching from the Tyne south to Ipswich. A further 177 flood alerts warning of possible flooding, covering rivers across western, central and northern England.
A fifth severe flood warning had earlier been issued for eastern Scotland as the emergency services grappled with substantial flooding from Storm Babet, which claimed its first fatality after a woman was swept away in Angus.
A flood duty manager for the Scottish Environment Protection Agency, Pascal Lardet, said Thursday's rainfall had been "exceptional" and flooding incidents were likely to increase during the day. We are in a very challenging, serious and potentially dangerous situation," he told BBC Radio Scotland.
On Thursday night a 57-year-old woman died after being swept into the Water of Lee in Glen Esk, Angus.
On Friday it emerged that the rescue services were searching for a man reportedly trapped in a vehicle caught in flood water near Marykirk in Aberdeenshire.
The five severe flood warnings are in the Angus and Aberdeenshire area covered by a rare red "danger to life" weather warning, which extends south to the outskirts of Dundee and Perth, as powerful winds from Storm Babet continued to lash the east coast of Scotland.
In Brechin, fire crews went door to door to rescue residents after flood barriers were breached. Hundreds of households had been told to evacuate on Thursday but some remained in their homes. Angus council said the flooding was the worst the town had experienced.
Jill Scott, a councillor for Brechin and Edzell, said that in some cases the flood currents were too strong for rescue boats to get to some houses.
"There will be hundreds of houses flooded," she said. "It unbelievable. It's devastating. I don't know what the council's going to do, to be honest - how many people they are going to have to rehome. People will have lost everything."
Major roads are closed by flooding, including sections of the A9 trunk road in the southern Highlands and the A90 at several places in Dundee and Aberdeenshire. The Tay Road Bridge, the Dornoch Bridge and Forth Road Bridge were closed to high-sided vehicles.
Train services have been suspended throughout the affected area, across Fife, Tayside, Perthshire and Aberdeenshire, with no trains running to Wick on the north coast either.
Ferry services in the inner Hebrides, to Shetland and within Orkney were also cancelled, as were regional air flights operated by Loganair.
The Met Office's weather warnings now cover nearly all of the UK's eastern seaboard, with yellow rain and wind warnings stretching up the east coast of England from Essex to Berwick and northwards into Scotland.
In eastern England, National Highways said the A15 Humber Bridge between North Lincolnshire and east Yorkshire had been closed to high-sided and vulnerable vehicles because of strong winds.
Flooding in Midleton, with the water as high as car windows in some places.
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