The landslide-caused accident happened late on Tuesday on the Tsiribihina River in the Menabe region.
"Of the 26 passengers, 16 did not survive," police said.
The boat had stopped late at night at Belo-sur-Tsiribihina, a village about 320 kilometres (200 miles) southwest of the capital Antananarivo, so that passengers could have a break, L'Express de Madagascar newspaper reported Thursday.
As it was mooring, a slab of the embankment broke off and crashed onto the vessel, police told the news site.
Two of the dead passengers were children, one aged nine and the other around five months, the site said.
Four of the victims belonged to the same family and were transporting two bodies in coffins at the time of the accident, it added.
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