Police investigations into a report of rape "should have been carried out better than they were", said a High Court judge, as he cleared a 57-year-old man of raping the daughter of his live-in lover.

No photographs had been taken by police of the interior of the cabin of the prime mover where the rapes had allegedly taken place. This would have been "important evidence", said Senior Judge Kan Ting Chiu.

Only photos of the exterior were taken and the vehicle was later scrapped.

The alleged victim, now 23, had claimed that over a period of two years, when she was between 15 and 16, the accused would drive her to a forested area in Punggol in a prime mover. She was molested and raped on the rear bench, behind the front driver's and passenger's seats, she said.

In court, she described the bench as having a "cushion" that could sit four persons. The cabin was furnished with curtains stretching along the side windows and the windscreen, she said.

But the accused disputed her description. He said dirty tools and equipment would be placed on the bench.

His employer, a prosecution witness, confirmed the equipment would take up half the seat and the inside of the cabin would be filthy with oil stains.

In his judgment, Justice Kan said that based on the description of the accused and his employer, the cabin was not a place where the accused could carry out the acts described by the alleged victim.

He noted that her description of the cabin was "confusing". She was also unable or unwilling to draw a sketch.

The judge also noted other "disquieting aspects" of her recounting of events.

Two incidents of sexual abuse allegedly took place in the family flat in 2010.

The alleged victim said one took place after the accused told her 13-year-old sister to leave the flat to buy lunch. But Justice Kan noted the sister had made no mention of this when she was on the stand, and she was not asked about it.

The alleged victim first told her boyfriend in 2010 about the alleged rape. He persuaded her to tell her mother, which she eventually did a year later in 2011.

The mother said the girl told her only that the accused had "touched" her and she did not want to go to the police, so nothing was done.

In December 2012, the alleged victim and her younger sister told their brother that the accused sexually abused them, and he made a police report.

Justice Kan said the alleged victim's description of the cabin, her contradictory accounts of the sex acts, and the lack of corroboration had a "negative impact on her credibility".

"When there are substantial flaws and shortcomings in the evidence as there are here, there will be reasonable doubts," he said.