In a statement yesterday, WCC, which held a watching brief for the case, said the remarks were "insulting" and "gender insensitive".
They added that the Justice Zamani Abdul Rahim's findings that the child may have "imagined" or "fantasised" also runs contrary to legal findings in other countries.
"Legal commissions in Australia and Ireland have concluded that children do not consistently confuse reality and fantasy.
"One report specifically states that it is very unusual for children to fabricate a series of events or to fantasize about a sexual assault," WCC representatives Mariam Lim, Prema Devaraj (left) and Melissa Mohd Akhir said in a joint statement.
Justice Zamani had on Tuesday overturned the conviction of Ewe Peng Lip, 49, for raping the girl, now eight, at a kindergarten in Bukit Dumbar between January and April 2008.
'Porn video fed child' fantasy'
The Star reported that in his 64-page decision, the judge said that the child could have imagined the act after watching a pornography video.
"If a sexual act had occurred, there would be definite tell-tale signs on her pai-pai (private parts)," he had reportedly said.
The daily also reported that the judge, in brushing aside the girl's testimony, had said it is "common knowlege" that children "cannot distinguish between facts and imagination or fantasy".
"We must not forget who is involved in this rape allegation, even if she is an adult, in which women have a tendency to exagerate about a sexual act," he was quoted as saying.
He also said that there was no phsyical identification of Ewe by the girl, who in her testimony two years ago said the assailant was "as tall as Uncle Ewe".
According to the WCC, Zamani had not appreciated that a child description of a sexual assault may be different from an adult's, and had thus waved away her testimony as "fantasy".
They added that his claim that women or a female child is more likely to exaggerate a sexual act, as compared to men is "insulting" to women and showed "a complete lack of understanding" when dealing with women and child victims of sexual crimes.
WCC added that Malaysian courts are "lagging" when it comes to evidential law, particularly for sex crime cases.
"If the court starts on a premise of disbelief, what chance do victims have for justice?" they asked.
'Rape victims parents disillusioned'
They added that the judge had also "dismissed" family members' testimonies as "repetitions and cannot be independent evidence" when it fact, children often disclose incidence of abuse to a trusted adult who is likely to be a family member.
They added that that corroboration of the child's testimony as required in the Evidence Act 1950 for a conviction, is "extremely difficult to fulfill given the nature of sexual crimes".
"Furthermore medical and other physical evidence are often lost through late reporting which is a common feature among sexual crime victims due to trauma and embarrassment experienced by the victims."
They also said that the prosecution could have proposed alternative charges like "attempted rape, outraging of modesty or sexual connection using an object", instead of rape.
Urging the prosecution to appeal, WCC said the judgement had "disillusioned" members of the public, including parents of child rape victims the NGO works with.
"(They) are in despair, questioning the chances of getting justice in court if the trial process is so heavily-weighted against their children.
"It is high time the government fulfills its duty in ensuring skillful investigation, effective prosecution, and an informed, sensitised judiciary," they said.