He is set to travel to Hiroshima and Nagasaki, two cities flattened by U.S. atom bombs at the end of World War II and meet those “who still carry the wounds of this tragic event in human history,” he said after his arrival.
It is the second visit to Japan by a pope, after John Paul II in 1981.
He also spoke out against nuclear weapons in Hiroshima and Nagasaki at the time, during the Cold War era.
Francis wanted in his youth to be a missionary in Japan. Less than 0.5 per cent of Japanese are Catholics.
He says he still shares a “sympathy and affection” for the country.
During his flight from Bangkok, where he spent several days on the first leg of his trip, Francis sent two similar telegrams of greeting to Chinese President Xi Jinping, as well as the president of Taiwan, Tsai Ing-wen.
The democratically-governed island is not recognised as a state by the Communist leadership in Beijing and is seen as a breakaway Chinese region.
The Vatican is one of 15 states around the world to confer diplomatic recognition on Taiwan, however, and Francis’ telegram was addressed to “Your Excellency Tsai Ing-wen, President of the Republic of China (Taiwan).”
The split dates back to the civil war in 1949 when defeated troops from the Chinese nationalist Kuomintang party fled to Taiwan from mainland China as the Communists swept to power.
The island is still officially called “Republic of China” as Taiwan sees itself as a successor to the republic that existed in China until that point.
On each of his journeys, the pope dispatches telegrams to the president of all the countries he flies over, sending them good wishes for health and peace.
The pope also sent Hong Kong’s leader Carrie Lam a similar telegram, in which he described the Chinese special administrative area as a “territory.”
He wished the seven million people of Hong Kong, who are have seen months of violent unrest, “peace and well-being.”