Thousands of migrants are believed to be stranded at sea, many with little or water.
It was not immediately clear if those offloaded near the city of Penang would be given refuge, said Zafar Ahmad, a Malaysian human rights activist. Their vessel was discovered hours after a maritime official warned that new arrivals would be given food, water and then sent on their way, unless their boats were sinking.
"We have to help refugees who need assistance and direct them to where they want to go," he said. "It goes against our principle to chase away refugee boats that enter our territory."
Southeast Asia, which for years tried to quietly ignore the plight of Myanmar's 1.3 million Rohingya, now finds itself caught in a spiraling humanitarian crisis that in many ways it helped create.
No countries want them, fearing that accepting a few would result in an unstoppable flow of poor, uneducated migrants.
But governments at the same time respected the wishes of Myanmar at regional gatherings, avoiding discussions of state-sponsored discrimination against the Rohingya.