The closure was caused by flooding in an area close to Kongens Nytorv station, but not in the station itself, Metro Service told the Ritzau newswire.
Nørreport and Christianshavn stations were still open, but the M1 and M2 section of Kongens Nytorv station was closed due to water in the tunnel, according to the Copenhagen Metro website.
It was still possible to change between the M1 and M2 lines at Christianshavn at noon on Thursday, although those heading north towards Vanløse will have to find alternate transport from Christianshavn.
According to the Copenhagen Metro website, Metro buses have been put in place between the two affected stations.
At the time of writing, the M3 and M4 lines were running as normal and trains from Nørreport were not affected.
There is so far no information on when the affected stretch will open again, although Metro Service told Ritzau that its technicians are working to localise the source of the flooding.
This story will be updated when more information is available.
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