Prosecutor Jakob Buch-Jepsen described the case as "very unusual and extremely gross".
The Nautilus UC3 was the site of the death of journalist Kim Wall. While a news release was posted online Tuesday, the actual wording of the charges is expected to be made public only next week.
"It's not just that we have the same grounds for arrest as before, but I think they are stronger than last time", Buch-Jepsen said, adding that Madsen should be detained during the hearing.
If found guilty, Madsen faces possible life in prison.
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Wall, a 30-year-old freelance journalist who was researching a story on the entrepreneur and aerospace engineer, went missing after Mr Madsen took her out to sea in his 17-metre submarine in August last year. Madsen has denied any sexual relations with Wall.
She was last seen aboard Madsen's 56-foot submarine as it left Copenhagen on August 10.
Peter Madsen (right) talked to a police officer after his submarine sank outside Copenhagen Harbor. Initially, he told authorities he had dropped Wall off on an island several hours after their voyage began. But he eventually said that she had died on board his vessel after a hatch unexpectedly collapsed, and that she had hit her head while she was climbing stairs in the submarine's tower.
Now, prosecutors say they believe Madsen either cut Wall's throat or strangled her before dismembering her body and throwing her body parts into the sea.
Wall's dismembered, naked torso was found on a southern Copenhagen shoreline in late August. Wall's decapitated head was found in October.
It is not clear whether the court can rule on the submarine's fate separately to Madsen's trial, which is due to conclude in the spring.