A man in his 50s died Saturday at a hospital in Porto, while a 57-year-old man died today in the capital Lisbon, the ministry said in a statement.
They were among nearly 40 people who suffered smoke inhalation or were injured in a stampede when the fire broke out.
The blaze, believed to have been caused by a wood-burning stove, occurred in the village of Vila Nova da Rainha, around 265 kilometres (165 miles) north of Lisbon.
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