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Thousands of passengers were left stranded after both runways were closed, and around 20 flights due to depart tonight were cancelled.
Runway One was shut for a short time for “emergency repairs”, an airport spokesman confirmed.
Runway Two remains closed due to thick fog, the Manchester Evening News reports.
It follows a series of delays and flight cancellations due to adverse weather.
A spokesman said: “As a result of the closure, there will be ongoing delays to clear the backlog of flights.
“Passengers are advised to check the status of their flight with their airline.”
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Brits are also stuck at foreign airports as inbound flights wait to take off.
Rick Lane wrote on Twitter: “Currently sat on a delayed plane with what feels like 20,000 kids on way back from Lapland unable to take off.”
Michael Norcross added: “Any idea when the FR3234 to Eindhoven will be leaving? My girlfriend and eight-month-old daughter are waiting to catch return back to Manchester and no one is giving them any idea.”
The freezing fog will likely spread to the south of England by the morning and may sabotage travel.
Forecaster Craig Snell told the Evening Standard: “Temperatures tonight in the south where the skies are clear could drop down to -1 or -3C, in the cloudier north 3 to 5C.
“Tomorrow it will be quite a foggy start in the south and east of England, it could be locally quite dense and could take quite a long time to clear.”
“This could make the morning commute to work quite tricky.”