Australian Maritime Safety Authority received a request for help from a person on board the boat this morning, about 120 nautical miles north of Christmas Island in an area believed to be in Australian waters, The Age reported.
Information from rescued passengers suggested as many as five people were unaccounted for and are believed to have gone down with the vessel. Their bodies had not been found, the report said.
There were no details of the nationalities of those missing, nor whether they were men, women or children.
By 3.30 pm (local time) 106 people were recovered from the water and two were said to have minor injuries.
AMSA said its search and rescue operation would continue.
The navy's HMAS Parramatta was joined by a merchant vessel in conducting the rescue operation.
Another navy ship is en route.
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