The death toll rose late Sunday after state governors in the two most affected states confirmed two more deaths from a series of mudslides that struck hillside communities.
The head of national emergency services previously put the death toll at 38, the vast majority of whom were found in Puebla state, while the remainder died in neighboring Veracruz, according to Reuters.
Rafael Morena Valle, governor of Puebla state, said canine units were searching for the missing, but the number of unaccounted for residents was unclear.
Images of the damage from Earl, broadcast on Mexican television, showed massive mudslides burying entire hillsides, trees felled and buildings creaking under collapsed walls and roofs.
On the Pacific coast, Mexico's Baja California peninsula braced for another major storm to strike as early as Monday.
Tropical Storm Javier was generating maximum sustained winds of 50 miles per hour (80 kph) Sunday night and was forecast to become a hurricane late Monday, the U.S. National Hurricane Center said in a statement.
The center of the storm was expected to strike the southern tip of Baja, home to the beach resort of Los Cabos, by Monday night, Reuters reported.
At least 25 of the deaths in Puebla state were confirmed Sunday near the town of Huauchinango in the rugged Sierra Norte de Puebla mountains, site of the worst destruction so far.
Eleven people have died in Veracruz, buried in landslides after intense rainfall and flooding struck the Gulf coast state after Earl crossed the Yucatan peninsula.
"We continue to monitor rivers that are above critical levels," Veracruz Governor Javier Duarte said in a post on Twitter Sunday.
Before striking Mexico, Earl battered Belize last Thursday, smashing car windows and punching holes in the roofs of Belize City's wooden houses. It also flooded parts of the coast.