During the 15-minute meeting, Min Aung Hlaing told the Pope of the "great responsibility of the country's authorities in this moment of transition" to democracy after years of military rule, a Vatican spokesperson said.
It is unlikely that the Pope made direct references to the Rohingya.
“Using the term ‘Rohingya’ is really a red flag in Myanmar,” says David Camroux, Senior Researcher with Sciences-Po in Paris.
“The military refused to use that term, Aung San Su Kyi refuses that term. The Rohingya are not considered as citizens of Myanmar, the Rohingya are not considered as one of the recognised ethnic nationalities, they have no citizens’ rights and they are virtually stateless.”
Suu Kyi's silence slammed
It is not clear if or when the Nobel prize winner, who is currently Myanmar’s de-facto leader after being under house arrest until 2012, will speak in defence of the Rohingya.
Some say this is because she is not really in control and is being used by the military as a figurehead to keep foreign investors happy.
But her critics say that that should not prevent her from protesting against the ongoing persecution that is well documented by the UN and human rights organisations.
“Aung San Su Kyi doesn’t control the military,” says Mark Farmaner, of the London-based Burma Campaign that fought for Aung San Su Kyi’s release from house arrest but now turned into her fiercest critic.“She cannot order them to stop the attacks."
But he points out that nothing obliges her to defend the military and to deny human rights violations are taking place.
“Journalists, government officials, British government, European government officials and people from all over the world are going to Bangladesh [where many Rohingya have taken refuge]. They are hearing eyewitness accounts of what’s taking place.
“We know there is mass rape. We know there are babies thrown into fire and burned alive, we know that there’ve been massacres and there’s mass graves and yet Aung San Su Kyi’s government still refuses to accept this has happened. And she is still denying and defending the military. So there is nothing that forces her to do that under the constitution or politically.
“This is her choice,” Farmaner insists.
Pope's visit may turn tide
Aung San Su Kyi's supporters say that the military will cite the slightest attempt to defend the Rohingya as proof that she is disloyal to her predominantly Buddhist constituency and be ammunition in the political struggle to get rid of her once again.
Pope may help dialogue
“She is in a difficult situation because even her attempts at religious dialogue are perceived as somehow a slight on Buddhism,” says Camroux.
“And she is a head of state in the context of rising ethno-nationalist Buddhist nationalism in Myanmar, so in defending the Rohingya is really for her to cut herself of from her political base. So perhaps adding the Pope’s moral voice in a country which is [a majority] Buddhist but still has a respect for other religious leaders may be helpful to her."
Last week Myanmar and Bangladesh signed a deal aimed at repatriating Rohingya refugees in two months.
But details of the agreement raise questions for Rohingya fearful of returning without guarantees of basic rights.
Pope Francis will travel on to Bangladesh on Thursday, where he will meet a group of Rohingya Muslims in the capital, Dhaka.