The Muslim-majority nation issued the deeply critical statement ahead of a planned solidarity march in Kuala Lumpur, expected to be led by Prime Minister Najib Razak.
Burma recently warned Malaysia that it must respect policy held by the Association of Southeast Asian Nations' (ASEAN) and not interfere in its internal affairs.
Yet Malaysia's foreign ministry in a statement: “The fact that only one particular ethnicity is being driven out is by definition ethnic cleansing.
“This practice must stop, and must be stopped immediately in order to bring back security and stability to the Southeast Asian region.”
The foreign ministry said that since hundreds of thousands of Rohingya had fled the largely Buddhist country in recent years, including around 56,000 to Malaysia, the issue was of international concern.
Malaysia’s language towards Burma has become increasingly stern in response to violence in the country’s northern Rakhine State, where there has been a army-led crackdown, sending hundreds fleeing across the border to Bangladesh.
Satellite imagery have revealed hundreds of buildings burned to the ground across multiple villages, with the true scale of destruction difficult to gauge because of government-imposed media and foreign aid restrictions.
A convoy carrying the former UN chief Kofi Annanarrived outside the Rohingya village of Wapeik on Saturday morning, which has seen signficant damage from fire.
But non-state media journalists were stopped by police from coming near the convoy or entering the village, an AFP photographer at the scene reported.
In recent weeks Rohingya women in the Rakhine state have alleged that Burmese soldiers have raped and sexually assaulted them at gunpoint.
The surge in violence was triggered by the killings of nine police officers at border posts on 9 October in Rakhine, home to some 800,000 Rohingya.
Several government officials blamed a militant Rohingya group for the attacks. Security forces then sealed off access to Maungdaw district and launched a counter-insurgency operation.
There have been no arrests, and a formerly unknown Islamist militant group has taken responsibility.
Burmese government officials deny that they are responsible for the attacks on the Rakhine district, and have alleged that the Rohingya are burning down their own houses.
But in November, a senior UN official John McKissick said Burmese security forces are striving towards the "ultimate goal of ethnic cleansing of the Muslim minority in Myanmar".
Homeless and helpless: The Rohingya Muslims of Rakhine state
Diplomats and United Nations officials have privately said the 9 October attacks and subsequent crackdown have dismantled years of work rebuilding trust between the Muslim and Buddhist communities in Rakhine after ethnic and religious violence broke out there in 2012, Reuters reported.
There has been disappointment that Nobel laureate Aung San Suu Kyi, whose party took power this year from the military, has failed to ease the suffering of the Rohingya.
Although, Ms Suu Kyi bowed to weeks of international pressure late on Thursday to appoint a commission to investigate the original attacks and the allegations of human rights abuses in the military operation that followed.
However, she raised eyebrows with her pick for the chief of the team, vice president Myint Swe, who headed the feared military intelligence under former junta leader Than Shwe.
Ms Suu Kyi has also appealed for understanding of her nation's ethnic complexities, and said the world should not forget the military operation was launched in response to attacks on security forces that the government has blamed on Muslim insurgents.
“I would appreciate it so much if the international community would help us to maintain peace and stability, and to make progress in building better relations between the two communities, instead of always drumming up cause for bigger fires of resentment,” Ms Suu Kyi told Singapore state-owned broadcaster Channel News Asia during a visit to the city-state on Friday.
“It doesn't help if everybody is just concentrating on the negative side of the situation, in spite of the fact that there were attacks against police outposts,” she said.