The ICC said in April that political violence had killed about 450 people and forced hundreds of thousands to flee
President Pierre Nkurunziza signed a decree on Tuesday for Burundi to quit the International Criminal Court, after parliament voted overwhelmingly last week to remove the country from the court's jurisdiction.
The move is unprecedented in a continent whose leaders often complain that the court disproportionately targets Africans.
On Oct. 12, only two lawmakers voted in favour of staying under the jurisdiction of the Dutch-based ICC, while 94 voted against and 14 abstained.
In April, the ICC opened a preliminary investigation into Burundi, focusing on killings, imprisonment, torture, rape and other sexual violence, as well as enforced disappearances.
Burundi's government was infuriated last month by a U.N. report that named officials accused of orchestrating the torture and killing political opponents.
Since then, Bujumbura has banned three U.N. investigators from its territory and condemned a U.N. decision to set up a commission of inquiry to probe the violence, which began last year after Nkurunziza decided to seek a third term in office.
Opponents said his candidacy violated the constitution and a peace agreement that ended a civil war in 2005. The opposition mostly boycotted the polls and Nkurunziza won a third term.
The ICC said in April that political violence had killed about 450 people and forced hundreds of thousands to flee.
Earlier on Tuesday, the head of its governing body, Sidiki Kaba, said he was concerned that would undermine "efforts towards the objective of universality" and called on Burundi to "engage in a dialogue”.
Since it was set up under the 1998 Rome Statute, the court based in The Hague has focused on prosecuting such politically-motivated crimes as genocide and crimes against humanity.
Most of its investigations and indictments have been of Africans, stirring criticism from many governments on the continent.
Nine out of 10 situations under investigation by ICC prosecutors are African. All five verdicts have dealt with African suspects from Congo, Central Arican Republic and Mali.
The decree signed by Nkurunziza, published in the presidency's website, said the decision would "come into immediate effect".