Independent NGOs were suspended for contesting Nkurunziza's plans for a third term.
Parcem was also initially suspended in 2015 but was allowed to resume its activities when its legal representative accepted conditions imposed by the authorities.
The East African state of Burundi has suspended the country's last independent civil rights group, accusing it of "disturbing peace and public order."
A ministerial order, seen by AFP on Tuesday, applies to an NGO called Parcem, which campaigns for good governance.
Its activities "are suspended" indefinitely, according to the document, signed by Interior Minister Pascal Barandagiye.
Burundi has been in crisis since 2015, when President Pierre Nkurunziza ran for a third term and was re-elected in elections boycotted by most of the opposition.
At least 1,200 people were killed and more than 400,000 displaced in violence that the UN says was mostly carried out by state security forces.
Independent NGOs were suspended for contesting Nkurunziza's plans for a third term. Parcem was also initially suspended in 2015 but was allowed to resume its activities when its legal representative accepted conditions imposed by the authorities.
Barandagiye said that despite several warnings, the organisation "worked on tarnishing the country's image, and its leaders on disturbing peace and public order."
Parcem – an acronym for the French words meaning World and Action for Awakening Consciences and the Evolution of Mentalities – had recently launched a campaign highlighting Burundi's economic crisis, notably giving figures on poverty that conflicted with official data.
Quoting World Bank statistics, it had said Burundi had the least direct foreign investment and lowest rate of industrialisation in the world.
Three Parcem activists were acquitted on appeal last December after having been given 10-year jail terms for "harming state domestic security" after they failed to invite members of the ruling party to a meeting.
All the leading opposition figures have fled the country, and some of the activists who have remained have been murdered or injured.
Last year, a campaigner was handed a 32-year jail term for taking part in protests.