Myanmar has stopped sending workers to Muslim-majority Malaysia as relations sour over a bloody military crackdown on the Buddhist country's Rohingya minority.

The move came after Malaysian Prime Minister Datuk Seri Najib Tun Razak lashed out at Myanmar's de facto leader Aung San Suu Kyi for allowing "genocide", during a rally in Kuala Lumpur that drew thousands of people.

The crowds were protesting against a military crackdown in Myanmar's western state of Rakhine that has pushed more than 20,000 Rohingya Muslims into Bangladesh.

Survivors have told AFP horrifying stories of gang rape, torture and murder at the hands of Myanmar security forces, while dozens have died trying to cross the river that separates the two countries.

Buddhist-majority Myanmar has long discriminated against the stateless Rohingya and the recent crisis has galvanised protests in Muslim countries around the region, including Malaysia.

"We want to tell Aung San Suu Kyi, enough is enough... We must and we will defend Muslims and Islam," Najib said at Sunday's 5,000-strong rally.

"The world cannot sit and watch genocide taking place."

A Malaysian government minister has also called for a review of Myanmar's membership of the regional ASEAN bloc.

Myanmar officials have denied the allegations of abuse and Suu Kyi has told the international community to stop stoking the "fires of resentment".

Late Tuesday Myanmar's immigration ministry said it had stopped issuing new licences for its nationals to work in wealthier Malaysia, for years a top destination for migrant labour.

"Myanmar has temporarily stopped sending workers to Malaysia from 6/12/2016 because of the current situation in Malaysia," it said in a statement, without elaborating.

Myanmar has also summoned Malaysia's ambassador to protest at Najib's accusations of ethnic cleansing.

"Such irresponsible remarks could worsen the already deepening polarisation between the two communities and violent extremism," Myanmar's foreign ministry said on Wednesday.

Malaysia already hosts tens of thousands of Myanmar workers, most of them in low-paid jobs in factories or the food and hospitality industries.

According to Malaysia, some 56,000 Rohingya have arrived on its shores in recent years, many taking perilous boat journeys to flee poverty and discrimination in Rakhine.

But on Tuesday former UN chief Kofi Annan, who heads a commission on troubled Rakhine, told reporters he thought the crisis would not split the region apart.

"I think it can be contained. There is a possibility here to contain what is going on," he told a news conference in Yangon at the end of a week-long visit.