Charles will represent the Queen, head of the Commonwealth, when prime ministers and presidents gather in Rwanda for the global summit.
The visit has been overshadowed by a recent report in the Times which claims Charles branded the Government’s policy to send migrants to Rwanda “appalling”.
The newspaper said a source had heard Charles express opposition to the policy several times in private, and that he was “more than disappointed” by it.
At the steps of the plane was the UK’s High Commissioner to Rwanda Omar Daair, Rwanda’s High Commissioner to the UK Johnston Busingye, Chogm special advisor Yamina Karitanyi and the Prime Minister’s special representative on the Commonwealth Lord Ahmad.
Ahead of Chogm the prince hailed the potential of the Commonwealth to make a difference on issues like climate change or providing opportunities for young people.
He said: “Taking shared responsibility to solve problems like these means the Commonwealth has the potential to make a profound difference in the lives of its citizens – and, in so doing, to be an unparalleled force for good in our world.”
The future king will carry out a full day of engagements on Wednesday when he will meet survivors and perpetrators of the Rwandan genocide.
In 1994 hundreds of thousands of members of the Tutsi community were slaughtered in Rwanda by ethnic Hutu extremists.
The issue of genocide and reconciliation is said to be very close to the prince’s heart and he will visit a village that was targeted.
The trip will be the first royal visit to Rwanda – one of a minority of the world’s nations the Queen has not visited.
Charles has been encouraged by former Rwandan footballer Eric Murangwa to visit a church outside the capital where the remains of tens of thousands of genocide victims are buried.
Mr Murangwa was sheltered from the killings by teammates, and Charles made him an MBE in recognition of his efforts raising awareness of the genocide against the Tutsi.
He is the founder of the organisation Football For Hope, Peace And Unity.
In April, Mr Murangwa was invited to watch as the prince planted a tree at Dumfries House in commemoration of the genocide victims.
Chogm will take place in Kigali following its postponement in 2020 and 2021 due to the Covid-19 crisis.
Charles last represented the Queen at the event in Sri Lanka in 2013 – a move that was interpreted as preparation for his future role as monarch – and in 2018 he was appointed the monarch’s designated successor as head of the Commonwealth.
The event, which is usually held in a different country every two years, brings together leaders from the 54 Commonwealth nations.