Many rapists are known to the victim
The inquiry, by the Inspectorate of Constabulary and the Inspectorate for the Crown Prosecution Service, has found that only one in 13 cases reported to the police results in a conviction.
The report authors want specialist rape prosecutors to be appointed.
The Crown Prosecution Service told the BBC the court process could be "very stressful", but promised forthcoming changes would help rape victims in court.
This analysis - of more than 1,700 rape crime reports in England and Wales - is the largest of its kind and highlights flaws in the justice process.
In 1977, one in three reported rapes led to a conviction.
In 1999, the figure had fallen to one in 13. Only one in five allegations gets to trial.
No single reason explains the "attrition" rate though there are far more cases now of "acquaintance rape".
'Minefield'
The report pinpoints failures in the way the police treat rape victims, including bad decision-making by both officers and lawyers, and not enough specialist prosecutors.
It also draws attention to poor treatment of rape victims who are children or who have learning difficulties.
The Rape Crisis Federation for England and Wales estimates that one in four women suffer rape or attempted rape and that 97% of victims knew their assailant.
Merlyn Nuttal is a rape victim who has campaigned for the rights of victims in the judicial process.
She said the report highlighted inconsistencies in how cases are investigated and how victims are treated in court.
In particular, Ms Nuttal wants specialised training for prosecutors and those coming into contact with the rape victim, to ensure a fair trial and proper support.
She told BBC Breakfast: "I was abducted from the street. It was actually attempted murder as well as sexual assault, so I was taken straight to hospital.
"But I did find there was a minefield of problems going through investigation and the Crown Prosecution Service, even though I was supported greatly by the police.
"But as the victim, I suddenly found out if you get your case to court you are the number one witness and you have very little rights in the court proceedings."
Ms Nuttal said in Canada the introduction of specialist prosecutors and training had improved convictions by 50%.
Skilled prosecutors
Nicola Reasbuck, a crown prosecutor in Newcastle, speaking on the same BBC programme, said the number of rape allegations made against people known to the victim had dramatically increased.
These accusations, she said, were very difficult to prove because they usually centred on the issue of consent, rather than whether sex had occurred.
She said: "The court process is very stressful for victims and I think it's extremely important that the CPS works with the other agencies such as the police, the courts and the Bar, to try to make the process less stressful.
And she added: "The only way we can improve things is by developing techniques for the presentation of evidence and putting more cases before the courts."
She said changes in July would give victims in court more protection and privacy when giving evidence.
And she emphasised that some skilled rape prosecutors were already working in specialist units.