An amber weather warning in eastern Scotland has been extended as heavy rain drenches parts of the country, with flooding leading to school closures and disruption on roads and railways.

The amber “heavy rain” alert, covering Aberdeen, Aberdeenshire, Angus and Perth and Kinross, warns some fast-flowing or deep floodwater is likely, “causing danger to life”.

It was originally in place until 3pm on Friday but the Met Office said this has been extended until 9pm as the rain is now “a little slower to ease than earlier expectations”.

Meanwhile, a yellow warning which was in place for a large part of eastern Scotland until 6pm on Friday has been extended until midnight.

Rail passengers are facing disruption as the rain has forced the closure of some stretches of track, while flooding has also affected roads.

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In Angus, all schools in Brechin, Montrose and Kirriemuir were closed due to localised flooding, as well as more than a dozen others.

Aberdeenshire said many roads were impassable or passable only with care, while 11 power cuts were affecting the area, in places including Inverurie and Kintore, Stonehaven, Portlethen and Hatton of Fintray.

Network Rail Scotland said the line between Aberdeen and Dundee was closed as it deals with “flooding at multiple sites along the route” while the line between Aberdeen and Inverness was closed at Dyce and at Huntly.

The East Coast Mainline was closed for a time between Dunbar and Reston but later reopened.

On Friday morning, a lane of the M9 westbound was closed at Junction two due to flooding, while in Fife the A92 was closed between the Parbroath Crossroads and Melville Lodges due to flooding, and in Dunfermline, Halbeath Road was shut with diversions in place.

Traffic Scotland said there were reports of vehicles becoming stuck in standing water on the A90 Southbound between Laurencekirk and Brechin and the road was later closed southbound at Stracathro.

Regional flood warnings are in place from the eastern Borders to Aberdeenshire, with the Scottish Environment Protection Agency warning Aberdeenshire and Angus could be particularly affected.

There were 29 flood warnings and nine flood alerts in place on Friday morning.

Transport minister Jenny Gilruth said: “The Met Office is warning us to expect a period of difficult weather in parts of eastern Scotland throughout Friday, with heavy rain likely to impact travel in the amber warning area in the north-east.

“The conditions could potentially bring disruption to the transport network, so it’s important people plan their journeys before they set off – particularly if they’re looking to use the trunk roads or travel by rail.”

Forecasters said that some areas of higher ground in the amber warning area could see a month’s worth of rain within a couple of days, with more than 100mm of rain, and even 150mm, possible in parts of the Grampians and Cairngorms.

Average rainfall for November in Aberdeenshire is 113mm, while for Angus it is 122.8mm.

Network Rail Scotland said journeys will take longer today on the East Coast Mainline between Edinburgh and the Borders, as well as between Aberdeen, Inverness and the Central Belt because of the “extremely high rainfall” which means train speeds need to be limited for safety.

Chief Superintendent Louise Blakelock, head of road policing, said: “As an amber warning for heavy rain has been issued, we are urging motorists to plan ahead and avoid unnecessary travel.

“The Met Office, Sepa and Traffic Scotland websites have valuable information about weather disruptions and we would advise people to check these sites before setting off on your journey.

“If you do need to drive, make sure you and your vehicle are suitably prepared by having sufficient fuel, waterproofs, warm clothing, food and water in the event you are delayed and be mindful of increased stopping distances when braking.”