A "misplaced belief" that false accusations of rape or domestic violence are commonplace may be undermining police and prosecutors' efforts to investigate such crimes, the director of public prosecutions has warned.

Keir Starmer QC, speaking as he published a study showing there were only a few false allegations during 17 months over 2011 and 2012, said police should not adopt "an over-cautious approach" because "of the understandable concern that some allegations are false".

In the aftermath of the Jimmy Savile scandal, and separate concerns about the handling of rape cases by two police forces, Starmer told the Guardian: "Because people recognise the devastating effect of false allegations and because they perceive there to be more false allegations than this report would suggest there are, arguably they adopt a cautious approach. If [that] leads to a more rigorous test being applied when people report rape or domestic violence, then that can lead to injustice for victims."

The study released on Wednesday by the Crown Prosecution Service (CPS) reveals that during the 17-month test period – when all false allegation cases were referred to the DPP – there were 5,651 prosecutions for rape and 111,891 for domestic violence in England and Wales.

By comparison, over the same timespan, there were only 35 prosecutions for making false allegations of rape, six for false allegations of domestic violence and three that involved false allegations of both rape and domestic violence.

"Victims of rape and domestic violence must not be deterred from reporting the abuse they have suffered," Starmer says in the foreword to the report. "We have worked hard to dispel the damaging myths and stereotypes which are associated with these cases.

"One such misplaced belief is that false allegations of rape and domestic violence are rife."

Starmer's latest comments – which relate primarily to adults – come in the week that Her Majesty's Inspectorate of Constabulary concluded that Savile's sexual abuse could have been stopped as early as 1964, but the police mishandled evidence and dismissed victims.

Last month, it emerged that police at a specialist sex crimes unit in Southwark, south London, had manipulated crime statistics by failing to record sexual assault allegations in 2008-09, according to a report by the Independent Police Complaints Commission. The Guardian has also revealed that the IPCC has raised concerns about the way police in south Wales have handled allegations of assaults after the deaths of four women in domestic violence incidents.

"The mere fact that someone did not pursue a complaint or retracted it, is not of itself evidence that it was false," Starmer said. The report's demonstration that false allegations were relatively rare is therefore highly significant, he said. "That's why the numbers are really important."

The CPS report, written by Alison Levitt QC, principal legal adviser to the DPP, also aims to dispel the prejudice that those who make repeated complaints about being victims of sexual crimes should not be believed. It states: "Research indicates that a person may be targeted precisely because s/he is vulnerable, and as a result there is every possibility that s/he may have been a victim of rape or other violence on more than one occasion."

False allegations can ruin reputations and devastate lives, Starmer added. "Such cases will be dealt with robustly and those falsely accused should feel confident that the criminal justice system will prosecute these cases wherever there is sufficient evidence and it is in the public interest to do so."

Of 159 suspects linked to allegedly false claims referred to the CPS between January 2011 and May 2012, 92% were women. Nearly half of them were 21 or under. One surprise was that in 38% of those investigations, the initial complaint of rape or domestic violence was made by someone other than the suspect. Among those under 18 it was 50% and often involved a parent.

"It was a feature of these cases that the suspect later reported that the whole thing had spiralled out of control and he or she had felt unable to stop the investigation," the CPS report says.

The exceptionally high levels of domestic violence revealed in the figures are in line with recent increases. Citizens Advice said last week it had seen an 11% increase in cases of domestic violence reported to it in the last three months of 2012, compared with the year before.

Starmer said: "I have raised concerns about [the levels of] domestic violence prevalent among young people, in particular young girls aged 16 to 19 are probably now most at risk. We may have a new generation [suffering from such abuse]. I have no reason to think this problem is reducing."

Following completion of the CPS study, false allegation cases involving rape and domestic violence will no longer routinely be referred to the DPP. "These cases will now be handled by [CPS] areas rather than headquarters, but we will continue to have an assurance regime where reports are sent in every six months," Starmer said.

Sample cases will be checked periodically to ensure they are being handled correctly, he added. He said he was confident that all of the prosecutions that took place during the 17 month period were correctly handled and necessary.

He responded to a letter in the Guardian from Women Against Rape and others who complained that "rape victims continue to be prosecuted" and that it "prevents victims from coming forward and encourages rapists to attack again".

In a new letter today, Starmer writes: "False allegations of rape are rare, but they can, and do, devastate the lives of those falsely accused and must be treated seriously. My guidance to prosecutors highlights the fact that these cases must be informed by wider circumstances, for example, a prosecution would be highly unlikely where a woman may have retracted a true allegation of rape in the context of an abusive relationship."

The CPS report highlighted increasing use of mobile phones in rape cases – as in all other areas of crime. There have been cases where offenders have sent pictures to humiliate victims.

It also pointed to occasions where those accused of rape recorded the incident to prove sex had been consensual. In one case referred to in the report, a group of men who had given a woman a lift home filmed her when they left her to prove she was unharmed.