Col. Schoombie van Rensburg said he had been “furious” at the disappearances and had ordered officers to be body-searched for the “expensive” watches.
The court was also shown a photo of Oscar Pistorius in blood-covered shorts.
Oscar Pistorius denies murdering his girlfriend Reeva Steenkamp last year, saying he mistook her for an intruder.
The prosecution says he intentionally shot Reeva Steenkamp after an argument at his house on February 14, 2013.
Col. Schoombie van Rensburg, who was initially in charge of the crime scene, said that when he first saw the watches he was worried about them and ordered them to be photographed because they “looked expensive”.
After returning to the main bedroom where a team of forensic experts was gathering evidence, the police officer realized one watch, said to be worth as much as $10,000 was missing. He said he was told Oscar Pistorius’ sister Aimee had come into the room and removed it.
After leaving the room again, another watch went missing, so he gave instructions for the police officers and their cars to be searched.
Col. Schoombie van Rensburg said that after that, everyone entering and leaving the scene was thoroughly searched and entered into a log, presented in court.
He said he told Oscar Pistorius he should file a complaint, while he opened a case of theft.
The former officer, who retired last year, also told the court he was angry when he saw a ballistics expert handling Oscar Pistorius’ 9mm pistol without any gloves, and told him to put some on.
The admissions call into question the police’s handling of the crime scene, in a case that is likely to hinge on sensitive forensic evidence, correspondents say.
Friday’s hearing has now been adjourned and the trial continues on Monday.
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