The deportations will start on June 30, Ismail Sabri said during a press conference, and follow similar moves to send migrants back to Indonesia, where around 1,000 cases have been diagnosed each day this week.
Some 2,500 Indonesians have been deported from Malaysia in recent weeks, the minister said, with another 4,200 to follow.
"Stern action" awaits those trying to enter Malaysia illegally, the minister warned, adding that that 1,057 would-be migrants had been arrested trying to slip into the country since May 1.
Malaysian police carried out several raids on migrants' residences in May.
Hundreds of those arrested and held in migrant detention centres were later diagnosed with the coronavirus.
Ismail Sabri said on Friday that the migrants awaiting deportation had tested negative.
The third-wealthiest country in South-East Asia, Malaysia's plantations and factories have long been a draw for job seekers from poorer neighbours.
Among those trying to enter, usually by boat, are members of the Rohingya minority group fleeing Myanmar and Bangladesh.
Prime Minister Muhyiddin Yassin told a Friday videoconference summit of the Association of South-East Asian Nations (ASEAN), a 10-country regional bloc, that "Malaysia is unfairly expected to do more to accommodate incoming refugees." - dpa
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