"The assumption is that the cause of the accident was the rough weather."
Later on Friday, Segreste said authorities had found two bodies, one male and one female, in the Oaxacan community of Pueblo Viejo based on information from a woman who said she had survived the wreck.
The woman said about 26 passengers had been aboard the boat, Segreste said.
Segreste said the local government in San Francisco del Mar reported that it had found 22 more bodies on the shore.
But he added that public safety officers hadn't been able to access the area because two rivers had flooded there.
If confirmed to be migrants, it could be evidence that smugglers are increasingly turning to boats to transport Central Americans through Mexico, avoiding highway checkpoints.
Many illegal migrants have been stranded and looking for other ways north since service was interrupted this year on two railway lines they once used to hitch rides north on freight trains.
In August, thousands of US-bound Central American migrants found themselves stranded near the Guatemala border after Connecticut-based Genesee & Wyoming Inc. withdrew from a 30-year concession to operate the Chiapas-Mayab line.
For decades, migrants had relied on the train to carry them from to the US-Mexico border.