Muhoza was detained by the National Intelligence Service last weekend in Burundi’s economic capital Bujumbura.
She was charged on Thursday and transferred to the notorious Mpimba prison, a judicial source said on condition of anonymity.
"The investigation is continuing but the prosecution has announced that she is being prosecuted for endangering the internal security of the state and for ethnic aversion," the source said.
Security services arrested the 42-year-old journalist after comments she allegedly made in a WhatsApp group of practitioners discussing an alleged distribution of machetes to Imbonerakure, members of the ruling CNDD-FDD party's youth league, according to her lawyer and relatives.
They accused the secret services of "inflicting corporal punishment on her during interrogations."
Muhoza was allegedly blindfolded and handcuffed during questioning, as well as beaten and only allowed one meal of rice and beans a day.
Authorities have not commented on these claims, following a request from AFP.
It is not the first-time journalists have been targeted in Burundi, a deeply impoverished nation which has a poor record for press freedom and human rights.
A coalition of organizations representing Burundian journalists said on Thursday it hopes Muhoza is released and called on other journalists to show solidarity with her.
Global press freedom group Reporters Without Borders, known by its French acronym RSF, on Monday voiced its concerns about her arrest and detention.
Last year, RSF ranked Burundi 114th out of 180 countries in terms of press freedom.
"Burundian journalists live in fear of being threatened, attacked or arrested," RSF says on its website.
In 2023, journalist Floriane Irangabiye was sentenced to 10 years in prison for "undermining the integrity of the national territory", although the grounds of the charge are unknown.
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