Australian Customs vessel Ocean Protector went to the aid of the asylum-seeker boat and had taken survivors to Christmas Island, Minister for Home Affairs Jason Clare was quoted as saying by the 'The Australian' newspaper.
"Initial reports indicate 95 people have been recovered from the water including two deceased persons and two critically injured persons," he said in a statement.
HMAS Maitland and aircraft remained in the area to continue the search effort.
An Australian Maritime Safety Authority (AMSA) spokeswoman said the boat overturned 14 nautical miles north of Christmas Island at 11.20am (AEDT) today.
"My understanding is that all of the asylum seekers were in the water when the Ocean Protector arrived," she said.
"The nationalities of those on board was not known," the paper said.