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Peter Madsen told the court that Swedish journalist Kim Wall had died in an accident and he had buried her at sea, changing his earlier statement the he dropped her off alive in Copenhagen
Police later told a press conference that it was still too early to identify the body - missing its head, legs and arms - that was found by a passing cyclist.
"It is clear that the police, like the media and everybody else, is speculating whether this female body is Kim Wall, but it is way too soon to tell," Copenhagen police spokesman Jens Moller said.
The case is being followed particularly closely by Danish and Swedish media but has drawn interest from around the world.
The body had been sent for forensic analysis while divers continued to search the area where it was found, Moller said.
Madsen has been charged with the manslaughter of Wall who has been missing since he took her out to sea in his 17-metre submarine on Aug. 10. He denies the charge.
He was rescued a day later after his UC3 Nautilus sank. Police found nobody else in the wreck.
Danish and Swedish maritime authorities are using divers, sonar and helicopters in the continued search for the body in Koge Bay, south of the city, and in the Oresund Strait between the two countries.
Madsen, an entrepreneur, artist, submarine builder and aerospace engineer, went before a judge on Saturday for preliminary questioning. The case is not open to the public to protect further investigation, police said.