Pope Francis held talks with Myanmar's military chief at the start of a four-day trip to a country facing global condemnation over its treatment of Rohingya Muslims.

The pontiff will also visit Bangladesh, where more than 620,000 Rohingya have fled to escape what Amnesty International has called "crimes against humanity".

Myanmar's army has denied accusations of murder, rape, torture and forced displacement that have been made against it.

The Pope's first meeting in Yangon was with military commander Senior General Min Aung Hlaing in St Mary's Cathedral in the heart of the southeast Asian nation's largest city.

"They discussed the great responsibility of authorities of the country in this time of transition," Vatican spokesman Greg Burke said after the talks.

The talks, which lasted 15 minutes, were followed by an exchange of gifts.

The army chief told the Pope that "there's no religious discrimination in Myanmar and there's the freedom of religion," according to a statement on the Facebook page of Min Aung Hlaing.

Members of ethnic minority groups in traditional dress welcomed Pope Francis at Yangon airport, and children presented him with flowers as he stepped off his plane.

He waved through an open window at dozens of children waving Vatican and Myanmar flags and wearing t-shirts with the motto of the trip, "love and peace".

Only about 700,000 of Myanmar's 51 million people are Catholic. Thousands of them travelled by train and bus to Yangon, and they joined crowds at several roadside points along the way from the airport to catch a glimpse of the Pope.

More than 150,000 people have registered for a mass that Pope Francis will say in Yangon on Wednesday, according to Catholic Myanmar Church spokesman Mariano Soe Naing.

"We come here to see the Holy Father. It happens once in hundreds of years," said Win Min Set, a community leader who brought a group of 1,800 Catholics from the south and west of the country.

"He is very knowledgeable when it comes to political affairs. He will handle the issue smartly," he said, referring to the sensitivity of the Pope's discussions about the Rohingya.

Large numbers of riot police were mobilised in Yangon but there were no signs of any protests.

The trip is so delicate that some papal advisers have warned him against saying the word "Rohingya", lest he set off a diplomatic incident that could turn the country's military and government against minority Christians.

The pope has already used the word Rohingya in two appeals from the Vatican this year.

Asked if he would say it in Myanmar, Mr Burke said the pontiff was taking the advice he had been given seriously, but added: "We will find out together during the trip, it is not a forbidden word."