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In the most recent accident, nine people are missing. On Wednesday, 10 people were killed and 25 went missing when an overloaded boat capsized.
All of the rescued passengers from the first boat were arrested under immigration laws, BBC News said.
Both of the boats were carrying Indonesians heading back to their home country for the Ramadan fasting month.
Malaysian maritime agency official Mohammad Zuhri said that the second boat, which sank on Thursday morning, capsized in waters off Sepang town on the outskirts of Malaysia's capital city Kuala Lumpur.
Mr Zuhri said 18 people, including four women, were rescued by passing merchant ships.
Officials said the boat was also believed to have been headed towards Indonesia's Sumatra island.