According to the United Nations, the total Rohingya refugee population in the area is now over 834,000.
In calls for peace in the country, he did not use the word Rohingya to describe the refugees, which is contested by the Rangoon government and military. Myanmar's Buddhist-majority population tends to use the word "Bengalis" to describe the minority Muslim group, viewing them as illegal immigrants from Bangladesh.
Activists have charged that Pope Francis was now complicit in the country's strategy to delegitimize the Rohingya because he did not use the term in Myanmar, CNN noted.
Since Aug. 25 about 621,000 Rohingya refugees have arrived in Bangladesh, fleeing violence in Myanmar.
He also called the world to action, saying "none of us can fail to be aware of the gravity of the situation, the huge toll of human suffering involved, and the precarious living conditions of so many of our brothers and sisters, a majority of whom are women and children, crowded in the refugee camps".
But the Vatican defended his silence, saying Francis wanted to "build bridges" with the predominantly Buddhist nation, while admitting that his efforts at diplomacy were not "infallible".
The Rohingya are an ethnic and religious minority who have been persecuted in Myanmar for decades.
Pope Francis celebrates huge outdoor Mass to ordain new priests in Bangladesh
The pontiff had previously been criticised for failing to mention the Rohingya directly while in Burma. The army says "clearance operations" are targeting militants who attacked security positions in August.
Pope Francis has ended a diplomatically tricky trip to Asia, seeking the forgiveness of Rohingya Muslim refugees in Bangladesh after his controversial decision to not directly refer to their plight when he visited their homeland, Myanmar.
Myanmar's military has denied the allegations. "Now, it is our shared responsibility to ensure for them a safe, sustainable and dignified return to their own home and integration with the social, economic and political life of Myanmar".
In the past, Francis has strongly condemned the "persecution of our Rohingya brothers", denounced their suffering because of their faith and called for them to receive "full rights". "But the fact that hundreds of thousands of Catholics turned out to welcome the pope showed the world they have freedom in the Buddhist-dominated country of which they are a part", the Buddhist monk said.
"When a people, a religion or a society turns into a "little world", they lose the best that they have and plunge into a self-righteous mentality of "I am good and you are bad", Francis said at the Notre Dame College, founded by Catholic priests.
Francis' first events Thursday in Muslim-majority Bangladesh were pure protocol: He visited the national martyrs' memorial and signed a visitors' book at the Bangabandhu Memorial Museum, located at the site where Bangladesh's independence leader, Sheikh Mujibur Rahman, and 31 members of his family were killed in a 1975 military coup.
Pope Francis on Friday, traded his popemobile for a rickshaw.
Information for this article was contributed by Julhas Alam and Nick Perry of The Associated Press.