By Wednesday, police matched DNA taken from Wall's toothbrush and hairbrush to the torso.
Madsen, who's been charged with manslaughter, said in a recent closed-door court hearing that Wall died in an accident while aboard his submarine and that he "buried" her at sea in an "unspecified place" south of Copenhagen.
Ms Wall's boyfriend alerted authorities on August 11 that the 40-ton sub, named the UC3 Nautilus, had not returned from a test run.
A day after taking Wall, 30, out on his submarine, the inventor was rescued after the vessel sank. He initially told investigators he dropped Wall off at a remote section of the port of Copenhagen on August 10, but later changed his story to say he buried her at sea at she died during an accident while aboard the submarine, which sank.
Madsen was arrested in connection with Wall's disappearance after his submarine sank off Denmark's eastern coast, an event police said they suspected the inventor had caused on objective.
Police believe the suspicious submariner deliberately scuttled the Nautilus, which was found the next day and brought to land for an investigation.
Investigators are not convinced by Madsen's latest account and suspect him of negligent manslaughter.More news: Indian railways chief steps down after deadly crashes
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After intense research in the sea, the trunk and weighted down by Kim Wall, including the limbs and head have been deliberately severed, was discovered on Monday in the bay of Køge, not far from the Danish capital, by a cyclist.
COPENHAGEN, Denmark | Journalist Kim Wall had reported on conflicts, crises and natural disasters around the world. They also confirmed they had found Wall's blood in the submarine, Møller Jensen told reporters.
"She was alive in ways that most of us can only dream of being alive".
The additional accusation will be used by prosecutors to make a case next month that Madsen face murder charges - he is now being held on preliminary charges of involuntary manslaughter that were brought against him before Ms Wall's torso was found.
Wall's former classmates at Columbia University Graduate School of Journalism in NY held a candlelight vigil Wednesday in her memory.
In an email to The Associated Press, the family said it received the confirmation of her death "with boundless sadness and dismay", adding "the tragedy has hit not only us and other families, but friends and colleagues all over the world".
Jose went to journalism school with Wall at Columbia University in NY. The torso belonged to a missing Japanese woman and this is a case that has never been solved.