Prince Harry was appointed to the governing board of African Parks (APN) in 2023 after seven years of involvement with the charity, which was set up to protect natural habits and wildlife.
Chadian Environment Minister Hassan Bakhit Djamous said the decision to cut ties came in response to "the resurgence of poaching and the severe lack of investment" including in infrastructure and anti-poaching efforts, "the failure of APN to respect key clauses of the agreements" and "recurring irreverence shown towards the government of Chad".
African Parks, which manages parks in 12 other countries including Angola, Malawi and Zambia, confirmed Chad had terminated its two management mandates there.
"African Parks has initiated discussions with the ministry to understand the government's position and to explore the best possible way forward in support of the continued protection of these critical conservation landscapes," it said in a statement.
It is the second time in 2025 that a charity linked to Harry has attracted negative headlines.
He stepped down from Sentebale, which he helped set up to help people with HIV and AIDS in Lesotho and Botswana, after a public row with its chair, Sophie Chandauka, who accused Harry and the trustees of bullying, misogyny and racism.
Britain's charity regulator said in August it had found no evidence of bullying.
Harry, who lives in California with Meghan and their two children, stopped working as a member of the British royal family in 2020.
14°C