A government spokesman said the 35-year-old mother – named by local media as Amba Bohora – and her two sons were found dead by family members and others from the remote town of Budhinanda on Wednesday morning.
Bajura District administrator Chetraj Baral said it was thought they died of smoke inhalation from a small fire they kept to stay warm in the cold mountainous region 250 miles (400km) northwest of the capital Kathmandu.
He said the hut barely had enough space for three people and that parts of the clothes they were wearing were also burned.
Mr Baral said an investigation was under way and that he was consulting with government lawyers on whether charges would be lodged against the family over the banned practice called chhaupadi, which is punishable by jail time.
Those who force women and girls into exile during menstruation could face up to three months in prison or a fine of 3,000 Nepalese rupees (£21).
The bodies of the mother and her children have been taken to a nearby hospital for a post-mortem examination.
According to The Himalayan Times, the Hindu tradition was outlawed in 2005 but continues in some remote villages in western Nepal.
Those who follow the practice believe women and girls staying at home during menstruation will displease the gods and bring misfortune as they are considered impure.
While in isolation, some women face extremely cold weather, attacks by wild animals, and often must live in unhygienic conditions.
Mr Baral said the government was now planning to send officials into the region to educate people about the practice.
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