"People need to keep an open mind about the policy, the critics need to keep an open mind about the policy," Johnson told reporters. British newspapers have reported that Charles had privately criticised the plans, under which asylum seekers will be deported to Rwanda.
"A lot of people can see it's obvious merits. So yeah, of course, if I am seeing the prince tomorrow, of course I am going to make that point," Johnson told reporters in Kigali for a meeting of Commonwealth leaders.
Asked if he would he defend it if Charles were to raise it, Johnson said: "Yes, it hasn't come up so far, of course."
According to the media reports, Charles was more than disappointed at the Rwandan plan, which he described as "appalling".
His office Clarence House, which previously said it would give no response to the "supposed anonymous private conversations", has declined to comment on Johnson's remarks.
It merely has said the prince remains politically neutral and that policy matters were for the government.
(Reporting by Andrew MacAskill, writing by Muvija; editing by William James)