In comments first reported by The Times, the Prince of Wales is said to have been frustrated by the deportation policy as he prepares to appear in Kigali as a representative of the Queen Elizabeth II later this month.
The comments put him at the centre of a likely clash with the UK government, as the royal family rarely comment publicly on political issues.
The UK’s new policy for failed asylum seekers – deporting them to Rwanda – won a court victory on Friday when a judge ruled the first flight could take off as planned next week.
The prince is understood to have said that giving Channel migrants a one-way ticket to Africa was “appalling”.
In the reported comments, a source heard Prince Charles expressing opposition to the policy.
“He said he was more than disappointed at the policy,” the source said. “He said he thinks the government’s whole approach is appalling. It was clear he was not impressed with the government’s direction.”
Prince Charles’s staff at Clarence House has said he was not trying to influence government policy.
“We would not comment on supposed anonymous private conversations with the Prince of Wales, except to restate that he remains politically neutral. Matters of policy are decisions for government,” a spokesman said.
The High Court in London ruled on Friday that the first Rwanda flight could take off next Tuesday after hearing from 31 people due to be deported. The Home Office is planning to schedule more flights this year.
The judge ruled against the request to block the flight and said: “I do not consider that the balance of convivence favours the grant of the generic relief.”
Campaigners expressed disappointment that the move to block the flight had failed at the first hurdle.
“The judgment today is devastating to those desperately trying to reconnect with family, escape war and torture and rebuild their lives in safety in the UK,” Lou Calvey, a refugee and asylum specialist, told The National.
A judicial review is still expected to go ahead and the applicants in court were given permission to appeal.
UK charities Care4Calais and Detention Action, along with a trade union representing the Border Force personnel, launched a legal bid to stop the first scheduled removals flight.
They argued that the plan breaches asylum seekers' human rights and say the government cannot justify its claim that Rwanda is a safe destination.
The final hearing on the legality of the policy will be heard in July.