Tens of thousands of Muslim Rohingya have fled their homes since a bloody crackdown by the Myanmar army in the western state of Rakhine sparked by a string of deadly attacks on police border posts in early October.
"The fact that only one particular ethnicity is being driven out is by definition ethnic cleansing," Malaysia's foreign ministry said in an unusually strongly-worded statement.
Myanmar has balked at such criticism, saying the Rakhine crisis is an internal issue -- but international pressure on the country is mounting.
That, the statement said, "makes this matter no longer an internal matter but an international matter".
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Today morning, a convoy carrying the former UN chief arrived outside the Rohingya village of Wapeik, which has seen signficant damage from fire.
Non state media journalists were stopped by police from coming close to the convoy or entering the village, an AFP photographer at the scene said.
Annan is not expected to brief the media until Tuesday -- after his visit to Rakhine ends.
But rights groups and Rohingya refugees who have made it to Bangladesh have accused the military of killing civilians and razing entire villages as a form of collective punishment.
The Rohingya have long faced persecution and government restrictions on movement that many have likened to apartheid.
Much of Myanmar views the Rohingya as illegal immigrants from Bangladesh even though many have lived there for generations.
"The Bengali people who brand themselves Rohingya are not Myanmar citizens," Parmaukkha, a nationalist monk, told a small group of supporters protesting outside Malaysia's Yangon embassy today afternoon.
Before the latest violence broke out, Myanmar's de facto civilian leader Aung San Suu Kyi formed a commission tasked with trying to solve the Rakhine crisis, headed by Annan.
That task has been made considerably harder since fighting broke out.
The Nobel Peace Prize winner has also been criticised for not defending the Rohingya.
Since winning an historic election last year, she has hardly spoken out on the issue.
But during a trip to Singapore this week she gave a rare interview in which she hit out at international criticism.