The government on Wednesday sent a verbal note to resident UN coordinator Garry Conille to transmit the message to the rights council's High Commissioner Michelle Bachelet in Geneva.
"All international staff must be immediately redeployed and the office has two months to pack up and close its doors," according to the high ranking source at the foreign ministry, speaking on condition of anonymity.
A UN source confirmed the information, but also asked not to be named.
"The Burundi government is growing more radical and defiant towards the international community," the source said, highlighting Bujumbura's boycott of an East African Community Summit in November.
The gathering of regional heads of state in Tanzania, was meant to focus on the ongoing political crisis in Burundi, after several rounds of mediation failed due to government refusing to meet with exiled opposition groups.
Summit in Tanzania postponed
Burundi's absence forced the postponement of the summit to December 27.
The country has been in crisis since April 2015 when President Pierre Nkurunziza announced he would seek a controversial third term in office, sparking civil unrest that has left 1,200 dead and over 400,000 displaced.
In October 2016 Burundi suspended co-operation with the UN's human rights office over its "complicity" in a report accusing Bujumbura of systematic abuses and warning of a risk of genocide.
In September this year Burundi threatened to quit the rights council altogether after another report pointed to crimes against humanity in the country.
In 2017 Burundi became the first nation to leave the International Criminal Court after it launched a probe into the alleged atrocities in the country.