The 80-year-old pope, the first to travel to Myanmar, received Senior General Min Aung Hlaing for a 15-minute meeting at the archbishop’s residence in Yangon, where the pontiff is staying during his visit.
At least 620,000 Rohingya have fled western Rakhine state to Bangladesh, describing rape, murder and arson at the hands of Min Aung Hlaing’s army and ethnic Rakhine Buddhist mobs.
The UN and US have accused the military of “ethnic cleansing” in a campaign sparked by attacks by a militant Rohingya group on police border posts in late August.
The army chief told the pope that “Myanmar has no religious discrimination at all. Likewise, our military too […] performs for the peace and stability of the country”, according to a Facebook post published by the general’s office a few hours after the meeting.
There is also “no discrimination between ethnic groups in Myanmar”, he added.
‘Moment of transition’
The Rohingya, who are denied citizenship, are not recognised as one of the Buddhist-majority country’s formal ethnic groups.
After the meeting a Vatican spokesman said the religious leader and the army chief had discussed the “great responsiblilty of the country’s authorities in this moment of transition”.
Myanmar was ruled by a junta for five decades until a civilian government led by Aung San Suu Kyi came to power last year. The army retains sweeping powers over security and political heft through a parliamentary bloc of seats.
The army crackdown on the widely reviled Rohingya looms large over the pope’s four-day trip to a country with a tiny Catholic minority.
Francis has called the Rohingya his “brothers and sisters” in repeated entreaties to ease their plight as the latest round of a festering crisis has unfolded.
Earlier on Monday he was welcomed at Yangon’s airport in a colourful ceremony led by children from different minority groups in bright bejewelled clothes, who gave him flowers and received a papal embrace in return.
Nuns in white habits were among devotees waving flags as his motorcade swept past the golden Shwedagon Pagoda.
“I saw the pope… I was so pleased, I cried!” Christina Aye Aye Sein, 48, told AFP after the pope’s convoy received a warm but modest welcome.
“His face looked very lovely and sweet… He is coming here for peace.”
Myanmar’s estimated 700,000 Catholics make up just over one per cent of the country’s 51 million people.
But around 200,000 Catholics are pouring into Myanmar’s commercial capital Yangon before a huge open-air mass on Wednesday.
“People came from all corners of the country, even if we could only see him for a few seconds,” Sister Genevieve Mu, an ethnic Karen nun, told AFP.