Francis spent his first full day in the Buddhist-majority country meeting its civilian leader, a day after hosting the military general in charge of the mission to drive Rohingya from the northern Rakhine state.
In a speech, he said Myanmar’s future depended on respecting the rights of all ethnic groups — a veiled reference to the crackdown that has sent more than 620,000 Rohingya into neighboring Bangladesh from where they have reported entire villages were burned and looted, and women and girls were raped.
He previously has prayed for "our Rohingya brothers and sisters," lamented their suffering and called for them to enjoy full rights, but the term “Rohingya” is avoided inside Myanmar because the ethnic group is not a recognized minority.
Several high-profile figures, including former U.N. Secretary General Kofi Annan and Myanmar Cardinal Charles Maung Bo, urged Francis not to utter the term, fearing a potential blow against Myanmar's tiny Catholic community.
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The pope said Maynmar's future "must be peace, a peace based on respect for the dignity and rights of each member of society, respect for each ethnic group and its identity."
He also called for a "democratic order that enables each individual and every group — none excluded — to offer its legitimate contribution to the common good."
Human Rights Watch expressed dismay after the speech, saying the treatment of Rohingya was part of a pattern of “shameless religious discrimination against minority religions like Christianity and Islam” in the country.
"The pope missed an important opportunity to tell Myanmar that every group has the right to self-identify, and to publicly refute the unconscionable pressure by Aung San Suu Kyi and the Myanmar military to deny the Rohingya their identity,” said Phil Robertson, the group’s Deputy Director, Asia Division.
Earlier, the pope met the commander responsible for the crackdown, Gen. Min Aung Hlaing.
The Vatican didn't provide details of the contents of the 15-minute "courtesy visit," except to say that “they spoke of the great responsibility of the authorities of the country in this moment of transition" and that the pair exchanged gifts.
Rohingya Muslims have long faced state-supported discrimination in Myanmar, and were stripped of citizenship in 1982, denying them almost all rights and rendering them stateless. They cannot travel freely, practice their religion, or work as teachers or doctors, and they have little access to medical care, food or education.
Myanmar's army denies accusations of rape, torture, murder and forced displacement.
The latest violence erupted in August, when Myanmar security forces responded to militant attacks with a scorched-earth campaign that has sent many Rohingya fleeing to Bangladesh, where the pope will also visit on his trip.
In 2015, Pope Francis angered Turkey when he used the word “genocide” to describe the World War I mass killings of Armenians by Ottoman Turks. The Turkish government, which denies that the deaths constituted a genocide, recalled its ambassador to the Vatican in protest.
Alastair Jamieson reported from London.
Claudio Lavanga is Rome-based producer and correspondent for NBC News.
Alastair Jamieson is a London-based reporter, editor and homepage producer for NBC News.