The 20-year-old winner of the Nobel Peace Prize urged Myanmar's State Counsellor and de-facto leader to act against the violence that has seen tens of thousands of people flee into neighbouring Bangladesh.
She also called on Pakistan, the country of her origin and where she was shot in the head by Taliban militants, to provide aid to the Muslim refugees.
"Over the last several years, I have repeatedly condemned this tragic and shameful treatment. I am still waiting for my fellow Nobel laureate Aung San Suu Kyi to do the same," she said in a statement.
"Stop the violence. Today, we have seen pictures of small children killed by Myanmar's security forces. These children attacked no-one, but still their homes were burned to the ground.
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"If their home is not Myanmar, where they have lived for generations, then where is it? Rohingya people should be given citizenship in Myanmar, the country where they were born."
Malala, who is set to begin her philosophy, politics and economics (PPE)course at Oxford University, was made the youngest ever UN Messenger of Peace earlier this year and was also the youngest person to win the Nobel Peace Prize aged 17 in 2014.
She became internationally known after the incident and relocated with her family to Birmingham for further rehabilitation.
"Other countries, including my own country Pakistan, should follow Bangladesh's example and give food, shelter and access to education to Rohingya families fleeing violence and terror," she added.
Last week, UK foreign secretary Boris Johnson had also urged Suu Kyi to curb the violence against Rohingya Muslims in Myanmar.
"Aung San Suu Kyi is rightly regarded as one of the most inspiring figures of our age, but the treatment of the Rohingya is alas besmirching the reputation of Burma," he had said.
About 58,600 Rohingya civilians have left Myanmar and fled to neighbouring Bangladesh.
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