The overloaded vessel, whose passengers included scores of teachers and university students, went down early Saturday on the Chindwin River in the Sagaing region.
Some 150 people were rescued after the ferry sank on its way to Monywa, a city around 72 kilometres (45 miles) to the south.
14 dead, scores missing in Myanmar ferry sinking
But officials who believe up to 250 may have been aboard fear the death toll could top 100 as they search through the boat.
Bloated corpses floated to the surface as searchers hauled the top part of the brightly painted ferry out of the water with cranes on Wednesday.
"The total death toll has now reached 53," Sa Willy Frient, the local director of social welfare and resettlement who is leading the operation, told AFP.
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"We are not sure if we can lift the whole sunken boat tonight. There could be many more dead bodies downstairs."
Local monks have held memorial services for the dead, most of whom are thought to be women.
At least four of the boat's staff have been arrested and will face legal action, according to local authorities.
Shipwrecks are common in Myanmar, a mostly rural and poor country with rudimentary transport infrastructure.
Many living along the nation's flood-prone river systems rely heavily on ferries, which are often overcrowded and poorly maintained.
The European Union said it was "deeply saddened" by the disaster, and expressed "heartfelt condolences" to the families and friends of the victims.
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