Oaxaca's state government later Friday released a statement saying three people were confirmed dead and 20 others missing following the shipwreck. It said there was one survivor and authorities were searching for bodies near the towns of San Francisco Ixhuatan and San Francisco del Mar, about 200 miles from the Guatemalan border.
It was not immediately possible to reconcile the different statements, but an official said that flooding was impeding access to some of the remote beaches.
Oaxaca state public safety secretary Sergio Segreste said 24 bodies had washed ashore.
"This morning, we got a report that a vessel carrying undocumented migrants had capsized or gone down," Segreste said. "The assumption is that the cause of the accident was the rough weather."
Segreste said later that authorities had found two bodies in the community of Pueblo Viejo based on information from a woman who survived the wreck.
Moises Hernandez, regional commander for ministerial police in Oaxaca, told reporters Friday that the survivor was a 24-year-old Honduran woman who said the ship departed from Guatemala. She said the ship capsized on Tuesday with more than 20 people aboard, according to Hernandez.
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 had not 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 U.S.-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 U.S./Mexico border.