A ministry order "provisionally suspends the activities of certain civil society organisations, that are facing judicial action for their role in crimes committed" since protests began in April, interior ministry spokesman Therence Ntahiraja told AFP.
The measure means "these NGOs are closed, they are banned from all activities... Until there is a legal decision on their actions," another ministry source said.
The 10 groups hit by the suspension operate in the areas of human rights, children's aid and the fight against corruption.
Burundi descended into violence in April after the head of state launched a now succesful bid for a third consecutive term in office, despite concerns over the legality of such a move.
At least 240 people have been killed and more than 200,000 have fled the country since.
The government blames a string of attacks on "armed criminals", but the UN has warned that Burundi risks sliding back into civil war after a dramatic rise in violence.
Some 300,000 people were killed in the conflict, which kicked off a year before a genocide of mainly Tutsi people in neighbouring Rwanda.
Increasingly the leaders of the Burundi civil groups targeted by the government have gone into exile.
Last week the prosecutor general blocked the bank accounts of these organisations, according to a judicial source.
Pacifique Nininahazwe, one of the leaders of the campaign against allowing the president to serve a third term, said the move to ban the activities of the groups was illegal.
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