When Pope Francis visits Myanmar in late November and early December he will be going into a maelstrom of racial conflict, war crimes, gang rape and ethnic purging bordering on genocide.

Despite a relatively small Catholic population, the Vatican confirmed reports the pontiff will visit Myanmar, sometimes referred by its old name Burma, from November 27 to 30, stopping in Yangon and in the capital, Naypyitaw and then going to the Bangladeshi capital, Dhaka, from November 30 to December 2.

The announcement on Monday came hours after Bangladeshi border guards pushed back thousands of Rohingya Muslims fleeing the worst violence in Myanmar in five years, with 104 people killed.

This incident typifies the struggle the Rohingya – one of the most persecuted people groups in the world.

Largely Muslim, 1.1 million live in Myanmar and claim their roots there go back centuries. But are not recognised by the largely Buddhist ruling government, are denied citizenship and systematically persecuted.

A series of coordinated attacks by Rohingya insurgents on security forces on Friday triggered fresh violence that led to thousands trying to flee into Bangladesh.

Bangladesh is already host to more than 400,000 Rohingya refugees who have fled Buddhist-majority Myanmar since the early 1990s and Dhaka has insisted it could not accept any more.

But the United Nations has urged Bangladesh's government to give Rohingya shelter as they face increasing persecution at home.

Reporters from Reuters saw women, some carrying children and the sick, fording the river, which at that location is less than 10 metres wide. Bangladeshi border guards permitted about half a dozen people at a time to cross to access a pile of donated medicines.

'We came here out of fear for our lives, but we can't cross. So we don't know what to do,' said Aung Myaing, from Taung Bro Let Way village, standing knee-deep in the river.

He said the military and ethnic Rakhine Buddhists were looting and setting fires to their villages, including by using grenade launchers.

When asked about insurgents he said: 'We didn't see them, we have no relation to them. But Myanmar doesn't distinguish between the terrorists and civilians. They are hunting all the Rohingya.'

For Myanmar's national leader Aung San Suu Kyo, hailed the country's saviour when elected in the credible poll for 25 years, the army's treatment of the Rohingya and her failure to stop it blights her records and international reputation.

Amnesty International have accused Myanmar's mainly Buddhist military of murder, rape, torture and looting in the Rohingya's northern state of Rakhine.

'Soldiers and police have randomly fired on and killed civilians, raped women and girls, torched whole villages and arbitrarily arrested Rohingya men without any information about their whereabouts or charges,' the report's summary read.

'These actions have been a form of collective punishment targeting Rohingya in northern Rakhine state, and may amount to crimes against humanity.'

The report comes after a separate UN official said Myanmar was conducting 'ethnic cleansing' against the Rohingya.

Pope Francis has met Aung San Suu Kyi twice, once in 2013 and a second time this May. His warm welcome to her may give him influence but their mutual respect may be strained when he undoubtedly speaks against her country's hidden horrors.

Additional reporting from Reuters.