According to a report by Human Rights Watch, their actions amount to crimes against humanity, including murder, persecution and deportation.
It relates to violence in Myanmar's western Rakhine state in June and October of last year, in which more than 200 people were killed, and over 100,000 displaced.
Human Rights Watch says government security forces did nothing to stop the violence, and even took part in it.
The report comes as the European Union lifts sanctions against the country and President Thein Sein is given a peace award - the 'In Pursuit of Peace Award' is from the International Crisis Group (ICG).
The award recognises individuals for their outstanding contributions to the advancement of peace and security and praises the Myanmar's president for his efforts to "bring us closer to a world free of conflict".
It found extensive state involvement and planning in the killings and destruction of property and that community leaders and Buddhist monks, also played a role in the killings, along with police and army personnel.
The report also criticised Thein Sein's government for failing to bring those responsible to justice.
Myanmar's government has denied the charges made in the report, and plans to publish its own findings.
The UN has described the Rohingya as one of the most persecuted minorities in the world.
Some historians say the group dates back centuries. And many Rohingya in Myanmar migrated from Bangladesh in the early 19th century - that was when Britain annexed Myanmar as a province of British India and brought over migrant Muslim labourers.
The UN estimates they number around 800,000. Most live in Myanmar's western Rakhine state, near the border with Bangladesh. But Myanmar's government does not recognise them as one of the nation's ethnic groups, and denies them citizenship.
To discuss the findings of the report, Inside Story's Ghida Fakhry is joined by guests: Maung Zarni, a visiting fellow at the London School of Economics, and founding member of the Free Burma Coalition; Alistair Cook, a visiting research fellow at the East Asian Institute of the National University of Singapore; and Mike Harris from the Index on Censorship, an international organisation that promotes and defends the right to freedom of expression.
"Is he (Thein Sein) deserving of this award? Well firstly, it is obviously not for peace that has already been achieved but it is for peace that could be achieved. What we are seeing with the release of this report or even what is happening in Kachin state or indeed some of the other ethic nationality areas as well - is that there is conflict still ongoing. At the moment the signs aren't there but the motivation ICG have for this award is positive reinforcement."
Alistair Cook, research fellow at the University of Singapore's East Asian Institute
