A man accused of rape was allowed to walk free and later kill two children as a result of a "disturbing" police policy to manipulate crime statistics by failing to record sexual assault allegations – a tactic that was employed in several more London boroughs than was officially admitted on Tuesday, the Guardian has learned.

An official report from the Independent Police Complaints Commission on Tuesday identified one London borough – Southwark – where the policy operated.

However, sources said that an internal police review in 2009 had identified five other areas where similar practices operated.

The resulting policy led to scores of women in boroughs such as Haringey having their allegations not classed as crimes instead of being investigated by police. When the practices were spotted by Metropolitan police chiefs and corrected, it led to a 25% spike in recorded sexual offences in a year, a rise of 469 recorded incidents, a source said.

Tuesday's report from the IPCC focused on the policy of a specialist Met sex crimes unit based in Southwark, south London, which was branded as "deeply disturbing".

The IPCC said the Sapphire unit in Southwark tried to persuade women who reported they had been sexually attacked to drop their cases.

It did so to boost its performance figures, which were among the worst in the Met.

The policy had disastrous consequences. A woman who made rape allegations against Jean Say in November 2008 did not have her case investigated.

Say went on to murder his daughter Regina, aged 8, and son Rolls, aged 10, with a carving knife, with police having missed the chance to take him off the streets. He was later jailed for life.

The IPCC report says a detective decided that the woman who earlier made rape allegations against Say had consented to sex. Thus no forensics were taken and the suspect was not even interviewed about the rape allegation.

According to the report: "There is no doubt from the evidence that the woman made an allegation of rape at Walworth police station which should have been believed and thoroughly investigated."

The IPCC also revealed other Met failings. It said that officers involved in alleged blunders – which left the serial sex attacker Kirk Reid free to assault an estimated 71 women – had not faced a disciplinary panel, despite the watchdog saying they should answer charges of gross misconduct.

Furthermore, two officers who should have faced discipline hearings were in fact promoted.

A protest letter from the IPCC deputy chair Deborah Glass to the Met, complaining about a "unhappy litany of delay and prevarication" in the failure to hold discipline hearings, did not receive a reply, the watchdog added.

The report was the IPCC's ninth into the Met's treatment of sexual violence victims.

Glass warned that the Met's repeated claims to have learned lessons after a series of blunders was hard to find credible. "Given the number of cases where the Met's response to victims has failed, either through individual officers' criminality or neglect or more systemic problems of training, priorities and resources, the response that 'lessons have been learned' begins to ring hollow," she said.

The Met said the scandal in Southwark has been ended. It ran from 2008 to 2009.

Women reporting sexual assaults would be questioned repeatedly by a detective about whether they had consented to sex. They were encouraged to withdraw their complaints, which boosted the unit's sanctioned detection rate.

The Sapphire unit's behaviour broke the force's policy that women were to be believed unless there was compelling evidence to the contrary.

The IPCC refused to say how many women had been affected by the practice. It said further investigation was hampered because of missing files, which disappeared during building works and due to an archiving system.

But solicitor Debaleena Dasgupta, who helps women who feel they have been failed by the criminal justice system, said the refusal to investigate legitimate rape claims was wider-reaching than one Sapphire unit.

"I have been approached by people who have been in the same position when dealt with by other parts of the Met – it's not just Southwark," she said.

The revelations about Southwark are the latest in a long line of police blunders in dealing with sexual violence cases.

In the case of John Worboys, the Met police missed chances to stop a man who drugged, raped and sexually assaulted over 100 women. He was arrested and released after a woman came forward in July 2007 and officers chose to believe his account, not hers. The victim said she had been "lied to and laughed at" by officers. Worboys was given an indeterminate sentence in April 2009.

A detective from another Sapphire unit was convicted last year of failing to investigate the alleged rapes and sexual assaults of 12 women by faking police reports, failing to pass on forensic evidence and not interviewing suspects.

Green party London Assembly member Jenny Jones said the Met was failing to honour repeated promises to end blunders in rape and sexual assault cases: "Despite the fine words of four Commissioners in the past 12 years, the Met is still underperforming badly for rape survivors and simply not doing their job of solving crimes and catching criminals."

In a statement, the Met said it had improved: "We have for some time acknowledged that previous investigation of rape and serious sexual assault in the MPS was below standard. The activities identified in this report came during that era and highlight specific issues within Southwark which resulted in unacceptable actions by local officers.

"It is as a result of such failings that we have made substantial changes to the investigation of rape and serious sexual assault, both in terms of structure and revised working practices."

The IPCC said discipline cases may be held against Met officers and at least one from another unit is facing a criminal investigation.