Madsen, 47, who is accused of premeditated murder, sexual assault and desecration of a corpse, has said her death was accidental since the first day of his trial on March 8th.
He said Wall, 30, died when a hatch fell on her head, but changed his story in October after autopsy concluded there had been no damage to the skull.
Madsen has admitted dismembering her body and throwing it overboard, but denies premeditated murder and sexual assault.
The self-taught engineer said the freelance journalist died when the air pressure suddenly dropped and toxic fumes filled his vessel on the night of August 10th, 2017, while he was up on deck.
Ditte Dyreborg, a prominent lieutenant commander with the Royal Danish Navy, said Madsen's explanations were implausible, if not impossible, as she spoke at Copenhagen City Court on Tuesday.
"We did not find anything. No CO (carbon monoxide), no CO2 (carbon dioxide), no NOx (nitrogen oxide). Which we would have if the submarine engine was running with carbon monoxide in it," said Dyreborg, who was the first to inspect the vessel on August 11th.
Dyreborg also said that the delay in testing air composition inside the sub, which resulted from Madsen having initially given a different story as to how Wall died, would not have affected results.
“It makes no difference when measurements are made, because the air in the submarine was not changed in the meantime,” she said.
The witness also said that exhaust fumes Madsen claims filled the vessel could not have caused life-threatening conditions.
Madsen's explanation of the accident also states that a drop in pressure inside the cabin, while he was on deck, prevented him from getting back inside to help Wall. He said that she must have switched the engines off herself, allowing him to get back inside once the pressure had stabilised, but not before the journalist had been poisoned by the fumes.
But Dyreborg said that explanation was improbable.
“I do not believe that Kim Wall was trapped inside the submarine and poisoned by exhaust fumes. There would have been clear signs on the filters if that was the case, and there were not,” the lieutenant commander said.
If the engines had stopped, it would have taken a long time before Madsen could open the hatch again, she also said.
She also doubted whether Wall, untrained in piloting the sub, would have been able to switch off the engines herself, according to DR's report from the courtroom.
Seemingly irritated and agitated, Madsen took notes during Dyreborg's testimony and whispered technical questions into his lawyer's ear, according to an AFP reporter at the scene.
A coroner told a March 22nd hearing that there was no conclusive evidence to prove Wall's cause of death beyond doubt, adding she was probably strangled or had her throat cut.
The coroner could however not rule out poisoning as a result of toxic fumes.
Madsen's lawyer Betina Hald Engmark questioned the relevance of Dyreborg's expertise on smaller and private submarines, concluding the lieutenant commander did not carry out any tests on the vessel's air filters.
The prosecution, which is seeking a life sentence for Madsen, claims he tortured and killed Wall as part of a sexual fantasy.
Wall's body parts, weighed down with metal objects, were recovered from waters off Copenhagen. She also had 14 stab wounds to her genital area.
The first hearings focused on the inner workings of the eccentric inventor described by psychiatric experts as "perverse" and with "psychopathic traits".
The verdict is expected on April 25th.