About 1,400 children were sexually exploited in Rotherham over a 16-year period, according to a report that concluded "it is hard to describe the appalling nature of the abuse that child victims suffered".

The uncompromising report on events in the South Yorkshire town between 1997 and 2013 said in more than a third of these cases the youngsters were already known to child protection agencies.

Warning also of "blatant" collective failures by the council's leadership, the report by Professor Alexis Jay prompted the resignation of the council's Labour leader.

Roger Stone, the leader, said: "Having considered the report, I believe it is only right that I, as leader, take responsibility on behalf of the council for the historic failings that are described so clearly in the report and it is my intention to do so.

"For this reason, I have today agreed with my Labour group colleagues that I will be stepping down as leader with immediate effect."

Despite Stone's resignation, chief executive Martin Kimber said no council officers will face disciplinary action.

Jay said she found examples of "children who had been doused in petrol and threatened with being set alight, threatened with guns, made to witness violent rapes and threatened they would be next if they told anyone".

Jay said: "They were raped by multiple perpetrators, trafficked to other towns and cities in the north of England, abducted, beaten and intimidated." She said she found girls as young as 11 had been raped by large numbers of men.

The report said failures of the political and officer leadership of Rotherham council over the first 12 years she looked at were blatant, as the seriousness of the problem was underplayed by senior managers and was not seen as a priority by South Yorkshire police. Jay said police "regarded many child victims with contempt".

These failures occured despite three reports between 2002 and 2006 "which could not have been clearer in the description of the situation in Rotherham".

She said the first of these reports was "effectively suppressed" because senior officers did not believe the data. The other two were ignored, she added.

The report said: "By far the majority of perpetrators were described as Asian by victims." But, she said, councillors seemed to think is was a one-off problem they hoped would go away and "several staff described their nervousness about identifying the ethnic origins of perpetrators for fear of being thought racist".

She added: "Others remembered clear direction from their managers not to do so."

The spotlight first fell on Rotherham in 2010 when five men, described by a judge as sexual predators, were given lengthy jail terms after they were found guilty of grooming teenage girls for sex. The prosecution was the first of a series of high-profile cases in the past four years that have revealed the exploitation of young girls in towns and cities including Rochdale, Derby and Oxford.

Following the 2010 case, the Times claimed that details from 200 restricted-access documents showed how police and child protection agencies in the South Yorkshire town had extensive knowledge of these activities for a decade, yet a string of offences went unprosecuted.

The allegations led to a range of official investigations, including one by the home affairs select committee.

Last year, the South Yorkshire police and crime commissioner, Shaun Wright, said there had been "a failure of management" at South Yorkshire police as he responded to a report into the force on this issue by Her Majesty's Inspectorate of Constabulary (HMIC).

The report concluded: "No one knows the true scale of the child sexual exploitation (CSE) in Rotherham over the years. Our conservative estimate is that approximately 1,400 children were sexually exploited over the full inquiry period, from 1997 to 2013."

In response, Rotherham council, which commissioned the report, said it accepted the findings, including the statement that failures "almost without exception" were attributed to senior managers in child protection services, elected councillors and senior police officers.

It accepted that failures were not down to "frontline social or youth workers who are acknowledged in the report as repeatedly raising serious concerns about the nature and extent of this kind of child abuse".

The council's chief executive, Kimber, said: "The report does not make comfortable reading in its account of the horrific experiences of some young people in the past and I would like to reiterate our sincere apology to those who were let down when they needed help."

"The report confirms that our services have improved significantly over the last five years and are stronger today than ever before.

"This is important because it allows me to reassure young people and families that, should anyone raise concerns, we will take them seriously and provide them with the support they need.

"However, that must not overshadow – and certainly does not excuse – the finding that for a significant amount of time the council and its partners could and should have done more to protect young people from what must be one of the most horrific forms of abuse imaginable."