The message, posted in English, was a possible reference ongoing violence between Buddhists and Muslims in the state of Rakhine, also called Arakan state.
The hacker's message said "those Muslims have a message of peace to the world but you are killing them. If you continue with the killing of Muslims, we will target all the worshipers of Buddha everywhere in the world ... and your country will be a hell."
The message included a photograph of charred bodies at an unidentified location, a report by the Myanmar news Web site Mizzima said.
The Myanmar government Web site also was down for several hours after the attack, Mizzima reported.
However, the state-run news Web site New Light of Myanmar didn't mention the alleged attack.
Mizzima's report of the hacking comes as the government and security authorities are struggling with increased tensions in Rakhine.
The violence started early June when 10 Muslims were killed by a mob who pulled them from a bus late one afternoon. By the end of July nearly 80 people had been killed in ethnic clashes.
Rakhine occupies most of Myanmar's west coast on the Bay of Bengal and is mostly Muslim has a relatively large Muslim population. Within Myanmar, Buddhists make up 89 percent of the population while Muslims and Christians make up around 4 percent each, U.N. estimates state.
Many of the Rohingya have connections to neighboring Bangladesh and the violence has created a tide of refugees across the border as well as within Myanmar.
The U.N. High Commissioner for Refugees estimated that around 80,000 people have been displaced in and around the Rakhine towns of Sittwe and Maungdaw where much of the violence took place.
"Most of them are living in camps for internally displaced people, with smaller numbers staying with host families in surrounding villages," the statement said.
Last month the U.N. High Commissioner for Human Rights Navi Pillay called for a "prompt, independent" investigation into alleged human rights violations in Rakhine.
Tomas Ojea Quintana, the United Nations' special rapporteur on human rights who returned this week from visiting Myanmar, said the Southeast Asian nation, formerly called Burma, needs to tackle these challenges for the success of democratic transition and national reconciliation.
The human rights situation in Rakhine state is serious," Quintana said in a statement at the end of his visit.
He called for an independent investigation into allegations of serious human rights violations, including alleged excessive use of force by security and police personnel.
"It is of fundamental importance to clearly establish what has happened in Rakhine state and to ensure accountability. Reconciliation will not be possible without this and exaggerations and distortions will fill the vacuum to further fuel distrust and tensions between communities," he said.
The state nationality of the Rohingya lies at the root of the tensions. At issue is how many of the Rohingya are legal immigrants, illegal immigrants and Myanmar-born Muslims.
To prevent other ethnic flash points, the Myanmar government must set up a functioning immigration system, Benedict Rogers, Asia Team Leader at the international human rights organization Christian Solidarity Worldwide, said.
The tensions are heightened by claims and counterclaims on all sides where the majority of alleged crimes aren't verifiable, said Rogers, writing on the Web site of the Democratic Voice of Burma, a non-profit Myanmar media organization based in Oslo, Norway.
"There is no doubt that both communities have suffered and perpetrators of violence on both sides must be brought to justice," he said.
"Without an independent, international inquiry and international monitors on the ground, it will be impossible to establish the truth and, as Mr. Quintana has said, hold the perpetrators accountable."
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