Chief investigator Hilton Botha told the Pretoria Magistrate's Court that, according to his preliminary investigations, he believed Pistorius knew Reeva Steenkamp was in the bathroom at the time of the shooting.
He also said the angle of the shot indicated Pistorius had his prosthetic limbs on when he fired – contrary to his affidavit.
While on the stand, Botha, acting for the prosecution against Pistorius who was arrested for murdering Steenkamp, said the gunman would have been in the bathroom, facing away from the basin.
Two phones and the firearm used in the incident were found on the carpet close to the shower door next to the toilet.
This was after a charge of possession of unlicensed ammunition was added to athlete Pistorius's murder docket.
Rounds for a .38 special firearm were found in a safe in Pistorius's room while police investigated the shooting of his girlfriend. Investigating officer Botha said Pistorius had a licence for a 9mm pistol. This was the firearm mentioned in Pistorius's affidavit on Tuesday when he explained how he shot Steenkamp.
The second day of the bail hearing for the Paralympic and Olympian reopened on Wednesday.
Pistorius arrived earlier in a police car from cells at the Brooklyn police station with a blue towel covering his head. Magistrate Desmond Nair apologised for a delay in the proceedings and said this was to make extra arrangements for the media in another room, which had taken some time.
Pistorius had last-minute consultations with his legal team to prepare for the next phase of his bail application at the Pretoria Magistrate's Court on Wednesday morning.
Pistorius told the court on Tuesday he shot the model and law graduate through a locked toilet door at his home, thinking she was an intruder.
The 26-year-old wept uncontrollably in court on Tuesday as defence lawyer Barry Roux read out an affidavit, in which the athlete described shooting Steenkamp (29) through the bathroom door in a blind panic, thinking she was an intruder.
In contrast, lead prosecutor Gerrie Nel painted a picture of a premeditated killing, a crime which carries a life sentence in South Africa. "If I arm myself, walk a distance and murder a person, that is premeditated," he told the packed courtroom on Tuesday.
In addition to the bail application, his lawyers would also have to make a new application to keep him at the police holding cells instead of a prison, with last week's order to that effect expiring on Wednesday.
His family was already inside the court, his brother Carl, a likeness of the international athlete, and his sister Aimee among them.
On Tuesday Pistorius told how Reeva had slept over and how he had shot through a toilet door, thinking there was an intruder in his house.
He then realised that Steenkamp had been in the toilet.
He denied the allegation that he had murdered her or that it was premeditated, as the state alleged.
"I deny the aforesaid [murder] allegation in the strongest terms," Pistorius said.
The hearing is expected to conclude by the end of the week. – Additional reporting by Sapa, Reuters