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The vessel, reportedly carrying undocumented migrant workers heading for Aceh in Indonesia, capsized after leaving Carey Island in Malaysia's Selangor state on Wednesday morning, the Indonesian Ministry of Foreign Affairs told CNN.
Local fishermen and firemen from the area managed to rescue 55 people, including men, women and children, while three Malaysian search and rescue ships have also been dispatched.
However, authorities say the rescue effort is being hampered by low tides.
Indonesia's Deputy Ambassador to Malaysia is en route to the scene near Banting in the Strait of Malacca.