The incident late on Wednesday reflected rising communal animosity.
A seven-member bench of Permanent People's Tribunal (PPT), holding proceedings on alleged atrocities and state crimes against the Rohingya, Kachins and other ethnic minority groups in Myanmar, said the Myanmar army was committing the crime in the "context of official duties".
According to the United Nations, hundreds of thousands of Rohingya have fled Myanmar since a renewed military crackdown began on August 25.
The human rights body said that while there have been no reported instances of deportations of UNHCR-registered Rohingyas from India, some refugees have reported instances of harassment.
Bhikkhu said the monks had not received any direct threats, but he had seen some on the internet.
Tin Maung Swe, secretary of the Rakhine state government, said requests from the two villages for safe passage had been denied, since they had enough rice and were protected by a nearby police outpost.
No aid workers were hurt, a spokeswoman for the International Committee of the Red Cross said.
The Muslim villagers said they wanted to leave but needed government protection from ethnic Rakhine Buddhists who had threatened to kill them.
Myanmar's civilian leader Aung San Suu Kyi was condemned early on in the crisis after photos of World Food Programme (WFP) food packages were shared on her office's Facebook page after apparently being seized from the Rohingya militants.
As the Narendra Modi government in its affidavit to the Supreme Court recently stated its plans to deport around 40,000 Rohingyas now staying in different parts of the country, the United Nations High Commissioner for Refugees (UNHCR) said that India was bound by law not to deport the refugees. This prompted criticism on Monday from fellow Nobel peace laureate Malala Yousafzai and Muslim countries in Asia targeting Suu Kyi.
Myanmar rejects that, saying its forces are tackling insurgents of the Arakan Rohingya Salvation Army who it has accused of setting the fires and attacking civilians.
The Hindu refugees say they are scared of going back to their villages in Buddhist-majority Myanmar's restive Rakhine state, but are also wary of staying in the mostly-Muslim Bangladesh.
Thousands of Rohingyas have poured into Bangladesh - and some into India - after fleeing a military offensive in Myanmar's Rakhine state.
It is with this understanding that we have recently agreed with Myanmar to provide financial and technical assistance for identified projects to be undertaken in Rakhine State in conjunction with the local authorities.
However, she did not address the United Nations accusations of ethnic cleansing by the military, which is in charge of security.
"In response to the situation in Myanmar, we are carefully reviewing content against our Community Standards", Budhraja added.
"Burma's senior military commanders are more likely to heed the calls of the worldwide community if they are suffering real economic consequences", said John Sifton, HRW's Asia advocacy director.
"Hundreds of thousands of refugees are living in an extremely precarious situation, and all the preconditions for a public health disaster are there", Onus said in a statement, calling for a "massive step-up of humanitarian aid".