At least four boats have sunk since last month as Indonesians, drawn to the relatively affluent Southeast Asian country for work, sought to go home for Eid al-Fitr, Islam's biggest festival, which starts in Malaysia on Monday.
The sinkings killed dozens and have left scores more missing.
Those wanting to return will be fined for being in Malaysia illegally, but will escape harsher prosecution, such as jail terms and caning, said a home ministry official who declined to be named as he is not authorised to make public statements.
"The legal way will be safer with less hassle, compared to risking their lives while paying a hefty fine to syndicates" smuggling the migrants via sea, he told the daily newspaper.
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An aide confirmed the comments.
In addition to the fine of at least 300 ringgit (USD 95), Indonesians have to pay 100 ringgit more for a one-way pass to return home.
The home ministry official did not say how much the maximum fine could be.
He added the programme was running from this month until the end of December, and could be extended to other nationals later.
But activists have warned that many will not be able to afford high fines, in addition to processing fees charged by private agents who are used by some migrants, to secure safe trips.
"My concern is that we do not have a very clear policy. It's not really service-oriented but rather profit-driven," Alex Ong of Migrant Care said, adding his group had received complaints by several migrants of being arrested despite the offer of a safe return.
Foreigners from neighbouring Indonesia and other mostly regional poorer countries are drawn by plantation, construction and other jobs shunned by Malaysians.
Boat accidents are common with three dead, eight missing and 10 rescued in the latest sinking off southern Malaysia on Thursday.
Both Malaysia and Indonesia are Muslim-majority countries with many observing the fasting month of Ramadan.
Eid al-Fitr marks the end of Ramadan and festivities run for several weeks.