At the meeting in Yangon on Tuesday, the pontiff stressed the importance of Myanmar respecting the "identity" of all of its ethnic groups, without using the term "Rohingya".
More than 600,000 Rohingya have fled to neighbouring Bangladesh in fear of abuses by Myanmarese soldiers.
The ethnic group is subject to a raft of discriminatory measures by Myanmar's government, such as being deprived of citizenship.
Having previously spoken against the "persecution of our Rohingya brothers and sisters," the leader of the Roman Catholic Church had been advised by Myanmar's archbishop not to use the word Rohingya.
Tun Khin, the president of the Burmese Rohingya Organisation UK (BROUK), told Al Jazeera that the pope's omission of the word "Rohingya" was "very sad".
"The Burmese government is denying our existence, and our identity," he said. "How can the pope raise the issue of the Rohingya crisis if he is not even using the name?"
Khin said that the pope should use his platform to pressure Aung San Suu Kyi and Myanmar's military to "stop this genocide" and to allow humanitarian aid access to the Rohingya.
"He should have spoken out against this hate campaign targeting the Rohingya and other minorities in Burma," Khin said.
Nevertheless, Al Jazeera's Scott Heidler, reporting from Yangon, said the pontiff did allude to the persecuted minority.
"Rohingya is a very sensitive topic, it is a very sensitive word here in Myanmar, particularly when it comes to dealing with the government," Heidler explained.
"He didn't say Rohingya but he alluded to the Rohingya and their plight, and he said that for the future of this country there needs to be acceptance and respect for the identity of all ethnic groups and who they are."
The International Rescue Committee expressed hope that the pope will address a number of key aspects regarding the Rohingya crisis.
“We are talking about a global figure of unity and compassion and hope for the world’s most vulnerable people,” Chiara Trincia, an IRC humanitarian expert told Al Jazeera.
Among these key aspects, Trincia said, is first and foremost the call for Myanmarese authorities to halt all military operations, and to emphasize that the crux of this crisis rests upon a recognition of and improvement in the basic and equal rights, services and protections long denied to the Rohingya people.
Myanmar's ruling party has objected to the use of the term Rohingya to identify the mostly Muslim minority, demanding that they are called "Bengalis" despite the persecuted group living there for generations.
The UN, as well as the US, have said the violent actions taken by Myanmar's armed forces and "local vigilantes" amount to "ethnic cleansing" against its Rohingya minority.
In 2012, Myanmar's armed forces began to force Rohingya into refugee camps, both in Rakhine state and across the border into Bangladesh.
The ongoing crisis is being described as the world's biggest forced exodus this year.
Last week the government of Bangladesh signed a deal with Myanmar on the repatriation of Rohingya, but details of the deal have still not been made public.