Press spokesperson with the Danish Defence Command (Værnsfælles Forsvarskommando) Christer Haven confirmed to broadcaster DR that the search for the vessel, lasting several hours, was now over.
After half a day's search, the Nautilus, the world's largest private submarine, was found sailing in Køge Bay.
The vessel went missing due to "technical difficulties" and it lost contact due to a bad radio connection, its owner, Peter Madsen who built the submarine in 2008 and was on board, told DR.
Madsen was accompanied by a Swedish journalist on the submarine, which was found after it eventually contacted Lyngby Radio, the Defence Command's centre for remote operation of 24 coastal radio stations in Denmark, reports Politiken.
The submarine left Copenhagen Harbour at 8:30pm on Thursday. It then failed to return to its dock at the Refshaleøen harbour at the scheduled time, prompting the Swedish journalist's partner to alert the Armed Forces at 2:30am, reports DR.
After around eight hours, the Danish military was able to announce the safety of vessel and the crew via Twitter.
The Armed Forces despatched boats and helicopters to search for the submarine, with the help of the Marine Home Guard.
The search team initially scoured Køge Bay, along with areas around southwest and east of the Amager and Saltholmen islands.
A file photo of the Nautilus. Photo: Bardur Eklund/Scanpix
The Forces then intensified their search in the Middelgrunden area off Nordhavn, having been informed that the owner of the submarine had planned to sail there, according to Politiken's report.
"We are incredibly happy to have found them safe and sound," Haven told Politiken.
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