The two leaders "praised the successful UK-Rwanda Migration and Economic Development Partnership, which is tackling dangerous smuggling gangs while offering people a chance to build a new life in a safe country," British Prime Minister Boris Johnson's Downing Street office said in a statement.
Their meeting on the sidelines of a gathering of Commonwealth nations followed talks in Kigali on Wednesday between Rwanda President Paul Kagame and the British heir to the throne Prince Charles, who has reportedly described the migrant deal as "appalling."
Rights groups, church leaders and the United Nations have also denounced the arrangement, which has threatened to overshadow the Commonwealth Heads of Government Meeting (CHOGM).
Both countries have defended the scheme, which involves Britain deporting asylum seekers to the east African country located thousands of miles away from Britain.
The UK said Wednesday it would introduce legislation allowing it to ignore certain decisions by the European Court of Human Rights after a judge in Strasbourg intervened to halt the first flight of asylum seekers to Rwanda that was due to take off last week.
The 54-nation Commonwealth club of mainly former British colonies has also been accused of turning a blind eye to Rwanda's record on human rights under Kagame, with critics saying it risks its credibility and integrity by hosting the summit in Kigali.
But Johnson was gushing in his praise of Rwanda's achievements.
"He congratulated President Kagame on Rwanda's extraordinary social and economic development in just a few decades, noting how pleased he was to be in the beautiful city of Kigali," the Downing Street statement said.
Johnson also welcomed Rwanda's "moral stance" on the war in Ukraine, it said, adding that the two leaders discussed ways to address the fallout from Russia's invasion, including the sharp rise in food prices which has hit African countries hard.