The survivor was recovered on Friday afternoon having spent more than a day in the water and was said to be in good health.
"Thirty-five more bodies have been recovered since Friday," said Mohamad Aliyas Hamdan, a Malaysian Maritime Enforcement Agency official.
We expect to find more over the next few days," he added.
Aliyas said the search operation would continue for the next three days, adding that from information gained from the 20 people rescued, there were believed to have been up to 80 people on the small vessel.
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The group were leaving Malaysia to return to Indonesia across the Malacca Strait.
Malaysia is Southeast Asia's third-largest economy and a magnet for migrant workers from its poorer neighbours, with the vast majority coming from Indonesia.
About two million Indonesians are now in Malaysia working a range of low-paid jobs.
Deadly accidents in the Strait are not uncommon, however, with travellers typically attempting the crossing in rickety vessels, often at night to avoid detection.