Rotherham council has been ordered to apologise to a whistleblower who helped to expose the town’s grooming scandal after council officials raided her charity without proper explanation – years after she risked imprisonment by revealing how the council, police and social services turned a blind eye to the abuse of at least 1,400 children.

Jayne Senior, who has worked with grooming victims since the 1999 in Rotherham and is now a Labour councillor, has been under investigation by the council since August 2016, two months after she was made an MBE for her services to child protection.

Her MP, Sarah Champion, said she was “appalled” it had taken so long to resolve. She questioned how much money had been spent investigating her.

The council has spent the last 20 months investigating complaints made by survivors of child sexual exploitation (CSE) who believe Senior earned up to £1m by charging for interviews about their plight and sharing information inappropriately, which she denies.

A few months before they made allegations against her she published her memoirs, called Broken and Betrayed. The book revealed how she became the whistleblower who risked imprisonment to provide evidence of their abuse at the hands of men of Pakistani origin.

Now the local government ombudsman has ordered Rotherham council to apologise to Senior and her charity, Swinton Lock, an arts and activity centre that sometimes works with CSE survivors.

The Guardian has seen a leaked copy of the report by the ombudsman, which found the council misled Senior about the progress of their investigation, keeping her waiting for a year to find out details of allegations made against her by three grooming victims.

The three women made a series of allegations to the council in August 2016, two years after they featured in Prof Alexis Jay’s report into Rotherham’s grooming problem.

On 13 December 2016, four months after the complaints were made, nine council officials visited Swinton Locks unannounced and carried out a “monitoring visit”, which those present view as a raid. They confiscated HR files and the laptop Senior was given by Rotherham council when she became a councillor in 2016.

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Champion described the number of people involved in the operation as “excessive”.

During the visit the officials refused to tell either Senior or the charity’s trustees why they were being investigated, saying they had not finished interviewing the complainants.

But the ombudsman found that they had in fact completed the complainants’ interviews four days before the raid, and yet waited another eight months, until 16 August 2017, to tell Senior what claims had been made against her.

The ombudsman, which looks at complaints about councils and social care providers in England, found the council was at fault for taking so long to investigate. It also said the council was at fault for misleading Senior about why she was being investigated.

In August 2016 the council said the complaints related to her current work with Swinton Lock. A year later the ombudsman found “the nature of the complaints had completely changed” and “the complaints were now wholly about the actions of [Senior], with some relating to her actions before she was employed by the charity”.

Champion said: “I’m appalled it’s taken so long. It’s crazy how ill informed she has been through the process. In the five years I have been an MP I have never come across something like this affecting a constituent, let alone a councillor and a well-known whistleblower. You would think that the council would be trying to do everything in a timely manner. In fact, the opposite has happened.”

In a statement Senior said: “As one of those who helped bring the Rotherham CSE scandal to light, I will continue to support children and families who were systematically failed by those whose statutory duty was to protect them and I will continue to work with the authorities to ensure justice is served. I welcome the Ombudsman’s decision but am disappointed that I have had to endure many months of unnecessary stress. Matters are now in the hands of our lawyers and consequently I cannot make any further comment.”

A spokeswoman from Rotherham council said: “The council received complaints from survivors of child sexual exploitation about the practice at Swinton Lock Activity Centre, which at that time was commissioned by the council to provide post-child-sexual-exploitation support to survivors and their families.

“Given the history of child sexual exploitation in Rotherham and the previous failure of agencies to properly support survivors, the council commissioned an independent investigation into complaints about Swinton Lock Activity Centre.”

She said the council had apologised in writing to the trustees of the charity and have complied with the agreed actions. “We are committed to completing the matter as soon as possible for all involved,” she said.

Senior helped reveal the systematic grooming and sexual exploitation of more than 1,400 children in Rotherham between 1997 and 2013 by handing over more than 200 restricted access documents to the Times in 2012.

The files showed that police and social services had been aware of extensive evidence of sex grooming by groups of men of Pakistani heritage for more than a decade. Offenders had been identified but no prosecutions followed.

The publication of Senior’s information shamed the council into commissioning an independent inquiry, led by Jay.

Her report, published in 2014, concluded that at least 1,400 children had been sexually exploited in Rotherham between 1997 and 2013.