The Duke of Sussex has announced his resignation as a patron of Sentebale, a Lesotho-based British charity which he co-founded, after a row between the trustees and the chair of its board.

Prince Harry said he had stepped down alongside co-founder and fellow patron Prince Seeiso of Lesotho and Sentebale's board of trustees after Dr Sophie Chandauka's relationship with the trustees "broke down beyond repair" and she sued the charity after she was asked to step down.

Dr Chandauka has reported the charity to the UK Charity Commission. She said she had "blown the whistle" about "abuse of power" and "harassment", and said her work was "in pursuit of the integrity of the organisation".

The Charity Commission says it is "aware of concerns about the governance" of Sentebale and is looking into them.

Sentebale was founded by Prince Harry and Prince Seeiso in 2006 with a focus on addressing the effects of HIV and Aids on young people in the southern African nations of Lesotho and Botswana.

In a joint statement, the princes said: "With heavy hearts, we have resigned from our roles as Patrons of the organisation until further notice, in support of and solidarity with the board of trustees who have had to do the same.

"It is devastating that the relationship between the charity's trustees and the chair of the board broke down beyond repair, creating an untenable situation.

"These trustees acted in the best interest of the charity in asking the chair to step down, while keeping the wellbeing of staff in mind. In turn, she sued the charity to remain in this voluntary position, further underscoring the broken relationship."

They would, they added, be "sharing all of our concerns with the Charity Commission as to how this came about".

Former trustees Timothy Boucher, Mark Dyer, Audrey Kgosidintsi, Dr Kelello Lerotholi and Damian West described their decision as "nothing short of devastating" for all of them.

They said they had lost trust and confidence in the chairwoman but her legal action meant they had no other option than to resign in the "best interest of the charity", as it could not take on the "legal and financial burden".

"This was not a choice willingly made, but rather something we felt forced into in order to look after the charity," they said.

Dr Chandauka said her work at Sentebale had been "guided by the principles of fairness and equitable treatment for all, regardless of social status or financial means".

"There are people in this world who behave as though they are above the law and mistreat people, and then play the victim card and use the very press they disdain to harm people who have the courage to challenge their conduct," she added.

This, she said, was the "story of a woman who dared to blow the whistle about issues of poor governance, weak executive management, abuse of power, bullying, harassment, misogyny, misogynoir – and the coverup that ensued".

The charity itself said it had "not received resignations from either Royal Patron" but it did confirm a "restructuring" of its board on Tuesday to bring in more experts "with the capabilities and networks to accelerate Sentebale's transformation agenda".

It said that it had announced plans last April to move from being a development organisation addressing the impact of HIV and Aids on children and young people in Lesotho and Botswana to "one that is addressing issues of youth health, wealth and climate resilience in Southern Africa".

"The recalibration of the Board is, therefore, part of Sentebale's ambitious transformation agenda," the charity added.

The Charity Commission said it was "aware of concerns" over Sentebale's governance, adding: "We are assessing the issues to determine the appropriate regulatory steps."