Herman Ouseley, the chair for 25 years of football’s anti-discrimination charity Kick It Out, announced he would stand down from the role because he was infuriated by his fellow trustees’ handling of personnel issues, the Guardian has learned.

Kick It Out, funded by the Football Association, Premier League, EFL and Professional Footballers’ Association, which each has a trustee on the board, is in some turmoil as it faces up to replacing Lord Ouseley, having just marked a quarter of a century since its formation in 1993 to combat racism in the game.

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The Charity Commission is due to start a “regulatory compliance case” after a group of former employees complained to it that Kick It Out’s trustees and senior management have not fostered an environment where staff can comfortably raise workplace concerns. One serious incident cited to the commission was a sexual assault suffered by a female member of staff, committed by a man from outside the organisation, in the evening of an away-day event. The woman did not want to report the assault to the police and was ultimately supported by an outside organisation to resolve the issues via restorative justice.

Kick It Out management are understood to have felt they tried to support the employee as well as they could, with time off and offers of counselling, but she felt they did not have the expertise and procedures in place to help her sufficiently. The former employees believe that the incident was so serious it should have been reported by the trustees to the Charity Commission but it was not until more than a year later.

One trustee in particular is understood to have begun making inquiries since the summer about the turnover of staff; in a small organisation 10 are understood to have left over the past couple of years. Gradually other trustees were informed there were staff concerns and the issue was put on the agenda for a meeting in September. Ouseley is understood to have been infuriated he was not included in the communications and deliberations before the meeting and that prompted his decision to announce his departure, which was confirmed after it leaked earlier this month.

He stands by the reasons he gave publicly, that he had been ready for several years to stand down having worked unpaid for so long at Kick It Out, but this issue prompted him to finally make the move.

The organisation’s chief executive, Roisin Wood, is understood to have defended the handling of the issues at that meeting of trustees in September. However, after the meeting she was suddenly taken seriously ill and has been off work since.

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The trustees have agreed to hold a review of the staff and personnel issues and are due to agree at a meeting in January how that review will be conducted.

The former employees are concerned more generally about the governance of Kick It Out, which is required to hold the football authorities and clubs to account over racism and discrimination, but relies on the game’s establishment to fund it, and as trustees. One former employee described this structure to the Guardian as “dysfunctional” and said staff are constrained in how strongly they can highlight issues. Ouseley, who has regularly spoken out strongly, has nevertheless long acknowledged this to be a tension.

The Charity Commission confirmed: “We have been made aware of concerns about the charity Kick It Out. We have opened a regulatory compliance case to assess these concerns.”

In a statement Kick It Out said: “The trustees take their responsibilities very seriously and have begun the process of an independent inquiry into the issues that have been raised. The trustees are made up of representatives from the football authorities, who naturally have an interest in how their money is being spent, but the board also has independent trustees, including the chair for the last 25 years, Lord Ouseley.”